/usr/lib/python2.7/dist-packages/PyMca/Elements.py is in pymca 4.7.4+dfsg-1.
This file is owned by root:root, with mode 0o644.
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# Copyright (C) 2004-2012 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# This file is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__revision__ = "$Revision: 2.00 $"
LOGLOG = True
import sys
import os
import numpy
import re
import weakref
import types
from PyMca import ConfigDict
from PyMca import CoherentScattering
from PyMca import IncoherentScattering
from PyMca import PyMcaEPDL97
from PyMca import PyMcaDataDir
"""
Constant Symbol 2006 CODATA value Relative uncertainty
Electron relative atomic mass Ar(e) 5.485 799 0943(23) x 10-4 4.2 x 10-10
Molar mass constant Mu 0.001 kg/mol defined
Rydberg constant R 10 973 731.568 527(73) m-1 6.6 x 10-12
Planck constant h 6.626 068 96(33) x 10-34 Js 5.0 x 10-8
Speed of light c 299 792 458 m/s defined
Fine structure constant alpha 7.297 352 5376(50) x 10-3 6.8 x 10-10
Avogadro constant NA 6.022 141 79(30) x 10+23 mol-1 5.0 x 10-8
"""
MINENERGY = 0.175
AVOGADRO_NUMBER = 6.02214179E23
#
# Symbol Atomic Number x y ( positions on table )
# name, mass, density
#
ElementsInfo = [
["H", 1, 1,1, "hydrogen", 1.00800, 1008.00 ],
["He", 2, 18,1, "helium", 4.00300, 0.118500 ],
["Li", 3, 1,2, "lithium", 6.94000, 534.000 ],
["Be", 4, 2,2, "beryllium", 9.01200, 1848.00 ],
["B", 5, 13,2, "boron", 10.8110, 2340.00 ],
["C", 6, 14,2, "carbon", 12.0100, 1580.00 ],
["N", 7, 15,2, "nitrogen", 14.0080, 1.25 ],
["O", 8, 16,2, "oxygen", 16.0000, 1.429 ],
["F", 9, 17,2, "fluorine", 19.0000, 1108.00 ],
["Ne", 10, 18,2, "neon", 20.1830, 0.9 ],
["Na", 11, 1,3, "sodium", 22.9970, 970.000 ],
["Mg", 12, 2,3, "magnesium", 24.3200, 1740.00 ],
["Al", 13, 13,3, "aluminium", 26.9700, 2720.00 ],
["Si", 14, 14,3, "silicon", 28.0860, 2330.00 ],
["P", 15, 15,3, "phosphorus", 30.9750, 1820.00 ],
["S", 16, 16,3, "sulphur", 32.0660, 2000.00 ],
["Cl", 17, 17,3, "chlorine", 35.4570, 1560.00 ],
["Ar", 18, 18,3, "argon", 39.9440, 1.78400 ],
["K", 19, 1,4, "potassium", 39.1020, 862.000 ],
["Ca", 20, 2,4, "calcium", 40.0800, 1550.00 ],
["Sc", 21, 3,4, "scandium", 44.9600, 2992.00 ],
["Ti", 22, 4,4, "titanium", 47.9000, 4540.00 ],
["V", 23, 5,4, "vanadium", 50.9420, 6110.00 ],
["Cr", 24, 6,4, "chromium", 51.9960, 7190.00 ],
["Mn", 25, 7,4, "manganese", 54.9400, 7420.00 ],
["Fe", 26, 8,4, "iron", 55.8500, 7860.00 ],
["Co", 27, 9,4, "cobalt", 58.9330, 8900.00 ],
["Ni", 28, 10,4, "nickel", 58.6900, 8900.00 ],
["Cu", 29, 11,4, "copper", 63.5400, 8940.00 ],
["Zn", 30, 12,4, "zinc", 65.3800, 7140.00 ],
["Ga", 31, 13,4, "gallium", 69.7200, 5903.00 ],
["Ge", 32, 14,4, "germanium", 72.5900, 5323.00 ],
["As", 33, 15,4, "arsenic", 74.9200, 5730.00 ],
["Se", 34, 16,4, "selenium", 78.9600, 4790.00 ],
["Br", 35, 17,4, "bromine", 79.9200, 3120.00 ],
["Kr", 36, 18,4, "krypton", 83.8000, 3.74000 ],
["Rb", 37, 1,5, "rubidium", 85.4800, 1532.00 ],
["Sr", 38, 2,5, "strontium", 87.6200, 2540.00 ],
["Y", 39, 3,5, "yttrium", 88.9050, 4405.00 ],
["Zr", 40, 4,5, "zirconium", 91.2200, 6530.00 ],
["Nb", 41, 5,5, "niobium", 92.9060, 8570.00 ],
["Mo", 42, 6,5, "molybdenum", 95.9500, 10220.00 ],
["Tc", 43, 7,5, "technetium", 99.0000, 11500.0 ],
["Ru", 44, 8,5, "ruthenium", 101.0700, 12410.0 ],
["Rh", 45, 9,5, "rhodium", 102.9100, 12440.0 ],
["Pd", 46, 10,5, "palladium", 106.400, 12160.0 ],
["Ag", 47, 11,5, "silver", 107.880, 10500.00 ],
["Cd", 48, 12,5, "cadmium", 112.410, 8650.00 ],
["In", 49, 13,5, "indium", 114.820, 7280.00 ],
["Sn", 50, 14,5, "tin", 118.690, 5310.00 ],
["Sb", 51, 15,5, "antimony", 121.760, 6691.00 ],
["Te", 52, 16,5, "tellurium", 127.600, 6240.00 ],
["I", 53, 17,5, "iodine", 126.910, 4940.00 ],
["Xe", 54, 18,5, "xenon", 131.300, 5.90000 ],
["Cs", 55, 1,6, "caesium", 132.910, 1873.00 ],
["Ba", 56, 2,6, "barium", 137.360, 3500.00 ],
["La", 57, 3,6, "lanthanum", 138.920, 6150.00 ],
["Ce", 58, 4,9, "cerium", 140.130, 6670.00 ],
["Pr", 59, 5,9, "praseodymium",140.920, 6769.00 ],
["Nd", 60, 6,9, "neodymium", 144.270, 6960.00 ],
["Pm", 61, 7,9, "promethium", 147.000, 6782.00 ],
["Sm", 62, 8,9, "samarium", 150.350, 7536.00 ],
["Eu", 63, 9,9, "europium", 152.000, 5259.00 ],
["Gd", 64, 10,9, "gadolinium", 157.260, 7950.00 ],
["Tb", 65, 11,9, "terbium", 158.930, 8272.00 ],
["Dy", 66, 12,9, "dysprosium", 162.510, 8536.00 ],
["Ho", 67, 13,9, "holmium", 164.940, 8803.00 ],
["Er", 68, 14,9, "erbium", 167.270, 9051.00 ],
["Tm", 69, 15,9, "thulium", 168.940, 9332.00 ],
["Yb", 70, 16,9, "ytterbium", 173.040, 6977.00 ],
["Lu", 71, 17,9, "lutetium", 174.990, 9842.00 ],
["Hf", 72, 4,6, "hafnium", 178.500, 13300.0 ],
["Ta", 73, 5,6, "tantalum", 180.950, 16600.0 ],
["W", 74, 6,6, "tungsten", 183.920, 19300.0 ],
["Re", 75, 7,6, "rhenium", 186.200, 21020.0 ],
["Os", 76, 8,6, "osmium", 190.200, 22500.0 ],
["Ir", 77, 9,6, "iridium", 192.200, 22420.0 ],
["Pt", 78, 10,6, "platinum", 195.090, 21370.0 ],
["Au", 79, 11,6, "gold", 197.200, 19370.0 ],
["Hg", 80, 12,6, "mercury", 200.610, 13546.0 ],
["Tl", 81, 13,6, "thallium", 204.390, 11860.0 ],
["Pb", 82, 14,6, "lead", 207.210, 11340.0 ],
["Bi", 83, 15,6, "bismuth", 209.000, 9800.00 ],
["Po", 84, 16,6, "polonium", 209.000, 0 ],
["At", 85, 17,6, "astatine", 210.000, 0 ],
["Rn", 86, 18,6, "radon", 222.000, 9.73000 ],
["Fr", 87, 1,7, "francium", 223.000, 0 ],
["Ra", 88, 2,7, "radium", 226.000, 0 ],
["Ac", 89, 3,7, "actinium", 227.000, 0 ],
["Th", 90, 4,10, "thorium", 232.000, 11700.0 ],
["Pa", 91, 5,10, "proactinium",231.03588, 0 ],
["U", 92, 6,10, "uranium", 238.070, 19050.0 ],
["Np", 93, 7,10, "neptunium", 237.000, 0 ],
["Pu", 94, 8,10, "plutonium", 239.100, 19700.0 ],
["Am", 95, 9,10, "americium", 243, 0 ],
["Cm", 96, 10,10, "curium", 247, 0 ],
["Bk", 97, 11,10, "berkelium", 247, 0 ],
["Cf", 98, 12,10, "californium",251, 0 ],
["Es", 99, 13,10, "einsteinium",252, 0 ],
["Fm", 100, 14,10, "fermium", 257, 0 ],
["Md", 101, 15,10, "mendelevium",258, 0 ],
["No", 102, 16,10, "nobelium", 259, 0 ],
["Lr", 103, 17,10, "lawrencium", 262, 0 ],
["Rf", 104, 4,7, "rutherfordium",261, 0 ],
["Db", 105, 5,7, "dubnium", 262, 0 ],
["Sg", 106, 6,7, "seaborgium", 266, 0 ],
["Bh", 107, 7,7, "bohrium", 264, 0 ],
["Hs", 108, 8,7, "hassium", 269, 0 ],
["Mt", 109, 9,7, "meitnerium", 268, 0 ],
]
ElementList= [ elt[0] for elt in ElementsInfo ]
from PyMca import BindingEnergies
ElementShells = BindingEnergies.ElementShells[1:]
ElementBinding = BindingEnergies.ElementBinding
from PyMca import KShell
from PyMca import LShell
from PyMca import MShell
#Scofield's photoelectric dictionnary
from PyMca import Scofield1973
ElementShellTransitions = [KShell.ElementKShellTransitions,
KShell.ElementKAlphaTransitions,
KShell.ElementKBetaTransitions,
LShell.ElementLShellTransitions,
LShell.ElementL1ShellTransitions,
LShell.ElementL2ShellTransitions,
LShell.ElementL3ShellTransitions,
MShell.ElementMShellTransitions]
ElementShellRates = [KShell.ElementKShellRates,
KShell.ElementKAlphaRates,
KShell.ElementKBetaRates,
LShell.ElementLShellRates,
LShell.ElementL1ShellRates,
LShell.ElementL2ShellRates,
LShell.ElementL3ShellRates,MShell.ElementMShellRates]
ElementXrays = ['K xrays', 'Ka xrays', 'Kb xrays', 'L xrays','L1 xrays','L2 xrays','L3 xrays','M xrays']
def getsymbol(z):
if (z > 0) and (z<=len(ElementList)):
return ElementsInfo[int(z)-1][0]
else:
return None
def getname(z):
if (z > 0) and (z<=len(ElementList)):
return ElementsInfo[int(z)-1][4]
else:
return None
def getz(ele):
if ele in ElementList:
return ElementList.index(ele)+1
else:
return None
#fluorescence yields
def getomegak(ele):
index = KShell.ElementKShellConstants.index('omegaK')
return KShell.ElementKShellValues[getz(ele)-1][index]
def getomegal1(ele):
index = LShell.ElementL1ShellConstants.index('omegaL1')
return LShell.ElementL1ShellValues[getz(ele)-1][index]
def getomegal2(ele):
index = LShell.ElementL2ShellConstants.index('omegaL2')
return LShell.ElementL2ShellValues[getz(ele)-1][index]
def getomegal3(ele):
index = LShell.ElementL3ShellConstants.index('omegaL3')
return LShell.ElementL3ShellValues[getz(ele)-1][index]
def getomegam1(ele):
return MShell.getomegam1(ele)
def getomegam2(ele):
return MShell.getomegam2(ele)
def getomegam3(ele):
return MShell.getomegam3(ele)
def getomegam4(ele):
return MShell.getomegam4(ele)
def getomegam5(ele):
return MShell.getomegam5(ele)
#CosterKronig
def getCosterKronig(ele):
return LShell.getCosterKronig(ele)
#Jump ratios following Veigele: Atomic Data Tables 5 (1973) 51-111. p 54 and 55
VEIGELE = True
def getjkVeigele(z):
return (125.0/z) + 3.5
def getjl1Veigele(z):
return 1.2
def getjl2Veigele(z):
return 1.4
def getjl3Veigele(z):
return (80.0/z) + 1.5
def getjm1Veigele(z):
return 1.1
def getjm2Veigele(z):
return 1.1
def getjm3Veigele(z):
return 1.2
def getjm4Veigele(z):
return 1.5
def getjm5Veigele(z):
return (225.0/z) - 0.35
def getjk(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjkVeigele(z)
ele = getsymbol(z)
if 'JK' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JK']*1.0
else:
return None
def getjl1(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjl1Veigele(z)
ele = getsymbol(z)
if 'JL1' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JL1']*1.0
else:
return None
def getjl2(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjl2Veigele(z)
ele = getsymbol(z)
if 'JL2' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JL2']*1.0
else:
return None
def getjl3(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjl3Veigele(z)
ele = getsymbol(z)
if 'JL3' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JL3']*1.0
else:
return None
def getjm1(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjm1Veigele(z)
ele = getsymbol(z)
if 'JM1' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JM1']*1.0
else:
return None
def getjm2(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjm2Veigele(z)
ele = getsymbol(z)
if 'JM3' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JM2']*1.0
else:
return None
def getjm3(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjm3Veigele(z)
ele = getsymbol(z)
if 'JM3' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JM3']*1.0
else:
return None
def getjm4(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjm4Veigele(z)
ele = getsymbol(z)
if 'JM4' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JM4']*1.0
else:
return None
def getjm5(z, veigele=None):
if z > 101:z=101
if veigele is None:
veigele = VEIGELE
if VEIGELE: return getjm5Veigele(z)
ele = getsymbol(z)
if 'JM5' in Scofield1973.dict[ele].keys():
return Scofield1973.dict[ele]['JM5']*1.0
else:
return None
def getLJumpWeight(ele,excitedshells=[1.0,1.0,1.0]):
"""
wjump represents the probability for a vacancy to be created
on the respective L-Shell by direct photoeffect on that shell
"""
z = getz(ele)
#weights due to photoeffect
jl = [getjl1(z), getjl2(z), getjl3(z)]
wjump = []
i = 0
cum = 0.00
for jump in jl:
if jump is not None:
v = excitedshells[i]*(jump-1.0)/jump
else:
v = 0.0
wjump.append(v)
cum += v
i+=1
for i in range(len(wjump)):
if cum > 0.0:
wjump[i] = wjump[i] / cum
else:
wjump[i] = 0.0
return wjump
def getMJumpWeight(ele,excitedshells=[1.0,1.0,1.0,1.0,1.0]):
"""
wjump represents the probability for a vacancy to be created
on the respective M-Shell by direct photoeffect on that shell
"""
z = getz(ele)
#weights due to photoeffect
jm = [getjm1(z), getjm2(z), getjm3(z), getjm4(z), getjm5(z)]
wjump = []
i = 0
cum = 0.00
for jump in jm:
if jump is not None:
v = excitedshells[i]*(jump-1.0)/jump
else:
v = 0.0
wjump.append(v)
cum += v
i+=1
for i in range(len(wjump)):
if cum > 0.0:
wjump[i] = wjump[i] / cum
else:
wjump[i] = 0.0
return wjump
def getPhotoWeight(ele,shelllist,energy, normalize = None, totals = None):
#shellist = ['M1', 'M2', 'M3', 'M4', 'M5']
# or ['L1', 'L2', 'L3']
if normalize is None:normalize = True
if totals is None: totals = False
w = []
z = getz(ele)
if z > 101:
element = getsymbol(101)
if z > 104:
elework = getsymbol(104)
else:
elework = ele
else:
elework = ele
element = ele
if totals and (energy < 1.0):
raise ValueError("Incompatible combination")
elif (energy < 1.0):
#make sure the binding energies are correct
if PyMcaEPDL97.EPDL97_DICT[ele]['original']:
#make sure the binding energies are those used by this module and not EADL ones
PyMcaEPDL97.setElementBindingEnergies(ele,
Element[ele]['binding'])
return PyMcaEPDL97.getPhotoelectricWeights(ele,
shelllist,
energy,
normalize=normalize,
totals=False)
elif totals:
totalPhoto = []
logf = numpy.log
expf = numpy.exp
for key in shelllist:
wi = 0.0
totalPhotoi = 0.0
if key != "all other":
bindingE = Element[elework]['binding'][key]
else:
bindingE = 0.001
if (key == "all other") and (key not in Scofield1973.dict[element].keys()):
doit = False
else:
doit = True
if doit and bindingE > 0.0:
if energy >= bindingE:
deltae = energy - bindingE
if key != "all other":
ework = Scofield1973.dict[element]['binding'][key]+deltae
else:
ework = energy
if ework > Scofield1973.dict[element]['energy'][-1]:
#take last
wi = Scofield1973.dict[element][key][-1]
totalPhotoi=Scofield1973.dict[element]['total'][-1]
else:
#interpolate
i=0
while (Scofield1973.dict[element]['energy'][i] < ework):
i+=1
#if less than 5 eV take that value (Scofield calculations
#do not seem to be self-consistent in tems of energy grid
#and binding energy -see Lead with e=2.5 -> ework = 2.506
#that is below the binding energy of Scofield)
if False and (Scofield1973.dict[element]['energy'][i] - ework) < 0.005:
#this does not work for Cd and E=3.5376"
print("Not interpolate for key = ",key,'ework = ',ework,"taken ",Scofield1973.dict[element]['energy'][i])
wi = Scofield1973.dict[element][key][i]
elif (key != 'all other') and Scofield1973.dict[element]['energy'][i-1] < Scofield1973.dict[element]['binding'][key]:
wi = Scofield1973.dict[element][key][i]
totalPhotoi = Scofield1973.dict[element]['total'][i]
elif Scofield1973.dict[element][key][i-1] <= 0.0:
#equivalent to previous case, solves problem of Fr at excitation = 3.0
wi = Scofield1973.dict[element][key][i]
totalPhotoi = Scofield1973.dict[element]['total'][i]
else:
#if element == "Fr":
# print "energy = ",energy," ework = ",ework
# print Scofield1973.dict[element]['energy'][i]
# print Scofield1973.dict[element]['energy'][i-1]
# print Scofield1973.dict[element][key][i]
# print Scofield1973.dict[element][key][i-1]
# print type( Scofield1973.dict[element][key][i-1] )
x2 = logf(Scofield1973.dict[element]['energy'][i])
x1 = logf(Scofield1973.dict[element]['energy'][i-1])
y2 = logf(Scofield1973.dict[element][key][i])
y1 = logf(Scofield1973.dict[element][key][i-1])
slope = (y2 - y1)/(x2 - x1)
wi = expf(y1 + slope * (logf(ework) - x1))
if totals:
y2 = logf(Scofield1973.dict[element]['total'][i])
y1 = logf(Scofield1973.dict[element]['total'][i-1])
totalPhotoi = expf(y1 + slope * (logf(ework) - x1))
w += [wi]
if totals:
totalPhoto += [totalPhotoi]
if normalize:
total = sum(w)
for i in range(len(w)):
if total > 0.0:
w[i] = w[i]/total
else:
w[i] = 0.0
if totals:
return w, totalPhoto
else:
return w
def _getFluorescenceWeights(ele, energy, normalize = None, cascade = None):
if normalize is None:normalize = True
if cascade is None:cascade = False
if sys.version < '3.0':
if type(ele) in types.StringTypes:
pass
else:
ele = getsymbol(int(ele))
else:
#python 3
if type(ele) == type(" "):
#unicode, fine
pass
elif 'bytes' in str(type(ele)):
#bytes object, convert to unicode
ele = ele.decode()
else:
ele = getsymbol(int(ele))
wall = getPhotoWeight(ele,['K','L1','L2','L3','M1','M2','M3','M4','M5','all other'],energy, normalize=True)
#weights due to Coster - Kronig transitions
#k shell is not affected
ck= LShell.getCosterKronig(ele)
if cascade and (sum(wall[1:4]) > 0.0) and (wall[0] > 0.0):
#l shell (considering holes due to k shell transitions)
#I assume that approximately the auger transitions give
#single equaly distributed vacancies
# I guess this will be better than ignoring them
if Element[ele]['omegak'] > 0.001:
auger = 0.32 * (1.0 - Element[ele]['omegak'])
#assume rest goes to other shells ...
cor = [auger,
auger + Element[ele]['KL2']['rate'] * Element[ele]['omegak'],
auger + Element[ele]['KL3']['rate'] * Element[ele]['omegak']]
w = [wall[1]+cor[0] * wall[0],
wall[2]+cor[1] * wall[0],
wall[3]+cor[2] * wall[0]]
else:
cor = 0.3 * wall[0]
w = [wall[1]+cor, wall[2]+cor, wall[3]+cor]
else:
#l shell (neglecting holes due to k shell transitions)
w = [wall[1], wall[2], wall[3]]
w[0] = w[0]
w[1] = w[1] + ck['f12'] * w[0]
w[2] = w[2] + ck['f13'] * w[0] + ck['f23'] * w[1]
wall[1] = w[0] * 1.0
wall[2] = w[1] * 1.0
wall[3] = w[2] * 1.0
#mshell
ck= MShell.getCosterKronig(ele)
if cascade and (sum(wall[4:]) > 0):
cor = [0.0, 0.0, 0.0, 0.0, 0.0]
augercor = 0.0
if wall[0] > 0.0:
#K shell
if 'KM2' in Element[ele]['K xrays']:
cor[1] += wall[0] * Element[ele]['KM2']['rate'] * \
Element[ele]['omegak']
if 'KM3' in Element[ele]['K xrays']:
cor[2] += wall[0] * Element[ele]['KM3']['rate'] * \
Element[ele]['omegak']
#auger K transitions (5 % total of shells M1, M2, M3)
cor[0] += wall[0] * 0.05 * (1.0 - Element[ele]['omegak'])
cor[1] += wall[0] * 0.05 * (1.0 - Element[ele]['omegak'])
cor[2] += wall[0] * 0.05 * (1.0 - Element[ele]['omegak'])
cor[3] += wall[0] * 0.01 * (1.0 - Element[ele]['omegak'])
cor[4] += wall[0] * 0.01 * (1.0 - Element[ele]['omegak'])
if sum(wall[1:4]) > 0:
#L shell
#X rays I can take them rigorously
mlist = ['M1','M2','M3','M4','M5']
i = 0
#for the auger I take 95% of the value and
#equally distribute it among the shells
augerfactor = 0.95/ 5.0
augercor = 0.0
for key in ['L1 xrays', 'L2 xrays', 'L3 xrays']:
i = i + 1
if i == 1:
omega=Element[ele]['omegal1']
auger= 1.0 - omega \
- Element[ele]['CosterKronig']['L']['f12'] \
- Element[ele]['CosterKronig']['L']['f13']
augercor += augerfactor * auger
elif i == 2:
omega=Element[ele]['omegal2']
auger= 1.0 - omega \
- Element[ele]['CosterKronig']['L']['f23']
augercor += augerfactor * auger
elif i == 3:
omega=Element[ele]['omegal3']
auger= 1.0 - omega
augercor += augerfactor * auger
else:
print("Error unknown shell, Please report")
omega = 0.0
#for the elements
#I consider Coster-Kronig for L1
if (i == 1) and (Element[ele]['Z'] >= 80):
#f13 is the main transition
if Element[ele]['Z'] >= 90:
#L1-L3M5 is ~ 40 %
#L1-L3M4 is ~ 32 %
#rest is other shells
cor[3] += 0.32 * wall[1] * \
Element[ele]['CosterKronig']['L']['f13']
cor[4] += 0.43 * wall[1] * \
Element[ele]['CosterKronig']['L']['f13']
if Element[ele]['Z'] > 90:
cor[2] += 0.5 * wall[1] * \
Element[ele]['CosterKronig']['L']['f13']
else:
#L1-L3M5 is ~ 43 %
#L1-L3M4 is ~ 32 %
#rest is other shells
cor[3] += 0.32 * wall[1] * \
Element[ele]['CosterKronig']['L']['f13']
cor[4] += 0.44 * wall[1] * \
Element[ele]['CosterKronig']['L']['f13']
#L2
elif (i == 2) and (Element[ele]['Z'] >= 90):
if Element[ele]['Z'] >= 94:
#L2-L3M5 ~ 3 %
#L2-L3M4 ~ 50%
cor[3] += 0.50 * wall[2] * \
Element[ele]['CosterKronig']['L']['f23']
cor[4] += 0.03 * wall[2] * \
Element[ele]['CosterKronig']['L']['f23']
else:
#L2-L3M5 ~ 6 %
cor[4] += 0.06 * wall[2] * \
Element[ele]['CosterKronig']['L']['f23']
elif (i==3):
#missing pages from article
pass
if key in Element[ele]:
for t in Element[ele][key]:
if t[2:] in mlist:
index = mlist.index(t[2:])
cor[index] += Element[ele][t]['rate'] * \
wall[i] * omega
cor[0] += augercor
cor[1] += augercor
cor[2] += augercor
cor[3] += augercor
cor[4] += augercor
w = [wall[4]+cor[0], wall[5]+cor[1], wall[6]+cor[2], wall[7]+cor[3], wall[8]+cor[4]]
else:
w = [wall[4], wall[5], wall[6], wall[7], wall[8]]
w[0] = w[0]
w[1] = w[1] + ck['f12'] * w[0]
w[2] = w[2] + ck['f13'] * w[0] + ck['f23'] * w[1]
w[3] = w[3] + ck['f14'] * w[0] + ck['f24'] * w[1] + ck['f34'] * w[2]
w[4] = w[4] + ck['f15'] * w[0] + ck['f25'] * w[1] + ck['f35'] * w[2] +\
ck['f45'] * w[3]
wall[4] = w[0] * 1.0
wall[5] = w[1] * 1.0
wall[6] = w[2] * 1.0
wall[7] = w[3] * 1.0
wall[8] = w[4] * 1.0
#weights due to omega
omega = [ getomegak(ele),
getomegal1(ele), getomegal2(ele), getomegal3(ele),
getomegam1(ele), getomegam2(ele), getomegam3(ele), getomegam4(ele), getomegam5(ele)]
w = wall[0:9]
for i in range(len(w)):
w[i] *= omega[i]
if normalize:
cum = sum(w)
for i in range(len(w)):
if cum > 0.0:
w[i] /= cum
return w
def getEscape(matrix, energy, ethreshold=None, ithreshold=None, nthreshold = None,
alphain = None, cascade = None, fluorescencemode=None):
"""
getEscape(matrixlist, energy,
ethreshold=None, ithreshold=None, nthreshold = None,
alphain = None)
matrixlist is a list of the form [material, density, thickness]
energy is the incident beam energy
ethreshold is the difference in keV between two peaks to be considered the same
ithreshold is the minimum absolute peak intensity to consider
nthreshold is maximum number of escape peaks to consider
alphain is the incoming beam angle with detector surface
It gives back a list of the form [[energy0, intensity0, label0],
[energy1, intensity1, label1],
....
[energyn, intensityn, labeln]]
with the escape energies, intensities and labels
"""
if alphain is None: alphain = 90.0
if fluorescencemode is None:fluorescencemode = False
sinAlphaIn = numpy.sin(alphain * (numpy.pi)/180.)
sinAlphaOut = 1.0
elementsList = None
if cascade is None:cascade=False
if elementsList is None:
#get material elements and concentrations
eleDict = getMaterialMassFractions([matrix[0]], [1.0])
if eleDict == {}: return {}
#sort the elements according to atomic number (not needed because the output will be a dictionnary)
keys = eleDict.keys()
elementsList = [[getz(x),x] for x in keys]
elementsList.sort()
#do the job
outputDict = {}
shelllist = ['K', 'L1', 'L2', 'L3','M1', 'M2', 'M3', 'M4', 'M5']
for z,ele in elementsList:
#use own unfiltered dictionnary
elementDict = _getUnfilteredElementDict(ele, energy)
outputDict[ele] ={}
outputDict[ele]['mass fraction'] = eleDict[ele]
outputDict[ele]['rates'] = {}
#get the fluorescence term for all shells
fluoWeights = _getFluorescenceWeights(ele, energy, normalize = False,
cascade=cascade)
outputDict[ele]['rays'] = elementDict['rays'] * 1
for rays in elementDict['rays']:
outputDict[ele][rays] = []
rates = []
energies = []
transitions = elementDict[rays]
for transition in transitions:
outputDict[ele][rays] += [transition]
outputDict[ele][transition]={}
outputDict[ele][transition]['rate'] = 0.0
if transition[0] == "K":
"""
if transition[-1] == 'a':
elif transition[-1] == 'b':
else:
"""
rates.append(fluoWeights[0] * elementDict[transition]['rate'])
else:
rates.append(fluoWeights[shelllist.index(transition[0:2])] * elementDict[transition]['rate'])
ene = elementDict[transition]['energy']
energies += [ene]
outputDict[ele][transition]['energy'] = ene
if ene < 0.0:
print("element = ", ele, "transition = ", transition, "exc. energy = ", energy)
#matrix term
formula = matrix[0]
thickness = matrix[1] * matrix[2]
energies += [energy]
allcoeffs = getMaterialMassAttenuationCoefficients(formula,1.0,energies)
mutotal = allcoeffs['total']
#muphoto = allcoeffs['photo']
muphoto = getMaterialMassAttenuationCoefficients(ele,1.0,energy)['photo']
# correct respect to Reed and Ware
# because there can be more than one element and
# I also weight the mass fraction
notalone = (muphoto[-1]/mutotal[-1]) *\
0.5 * outputDict[ele]['mass fraction']
del energies[-1]
i = 0
for transition in transitions:
trans = (mutotal[i]/sinAlphaOut)/(mutotal[-1]/sinAlphaIn)
trans = notalone * \
(1.0 - trans * numpy.log(1.0 + 1.0/trans))
if thickness > 0.0:
#extremely thin case
trans0 = notalone * thickness * mutotal[-1]/sinAlphaIn
trans = min(trans0, trans)
rates[i] *= trans
outputDict[ele][transition]['rate'] = rates[i]
i += 1
outputDict[ele]['rates'][rays] = sum(rates)
#outputDict[ele][rays]= Element[ele]['rays'] * 1
peaklist = []
for key in outputDict:
rays = []
if 'M xrays' in outputDict[key]:
rays += outputDict[key]['M xrays']
if 'L xrays' in outputDict[key]:
rays += outputDict[key]['L xrays']
if 'K xrays' in outputDict[key]:
rays += outputDict[key]['K xrays']
for label in rays:
if fluorescencemode:
peaklist.append([outputDict[key][label]['energy'],
outputDict[key][label]['rate'],
key+' '+label.replace('*','')])
else:
peaklist.append([energy - outputDict[key][label]['energy'],
outputDict[key][label]['rate'],
key+' '+label.replace('*','')])
return _filterPeaks(peaklist, ethreshold = ethreshold,
ithreshold = ithreshold,
nthreshold = nthreshold,
absoluteithreshold = True,
keeptotalrate = False)
#return outputDict
def _filterPeaks(peaklist, ethreshold = None, ithreshold = None,
nthreshold = None,
absoluteithreshold=None,
keeptotalrate=None):
"""
Given a list of peaks of the form [[energy0, intensity0, label0],
[energy1, intensity1, label1],
....
[energyn, intensityn, labeln]]
gives back a filtered list of the same form
ethreshold -> peaks within that threshold are considered one
ithreshold -> intensity threshold relative to maximum unless
absoluteithreshold is set to True
The total rate is kept unless keeptotal rate is set to false (for instance for
the escape peak calculation
"""
if absoluteithreshold is None:absoluteithreshold=False
if keeptotalrate == None:
keeptotalrate = True
div = []
for i in range(len(peaklist)):
if peaklist[i][1] > 0.0:
div.append([peaklist[i][0],[peaklist[i][1],peaklist[i][0]],peaklist[i][2]])
#div =[[peaklist[i][0],[peaklist[i][1],peaklist[i][0]],peaklist[i][2]] for i in range(len(peaklist))]
div.sort()
totalrate = sum([x[1] for x in peaklist])
newpeaks =[div[i][1] for i in range(len(div))]
newpeaksnames=[div[i][2] for i in range(len(div))]
tojoint=[]
deltaonepeak = ethreshold
mix = []
if len(newpeaks) > 1:
for i in range(len(newpeaks)):
#print "i = ",i,"energy = ",newpeaks[i][1], \
# " rate = ",newpeaks[i][0], \
# "name = ",newpeaksnames[i]
for j in range(i,len(newpeaks)):
if i != j:
if abs(newpeaks[i][1]-newpeaks[j][1]) < deltaonepeak:
if len(tojoint):
if (i in tojoint[-1]) and (j in tojoint[-1]):
#print "i and j already there"
pass
elif (i in tojoint[-1]):
#print "i was there"
tojoint[-1]+=[j]
elif (j in tojoint[-1]):
#print "j was there"
tojoint[-1]+=[i]
else:
tojoint.append([i,j])
else:
tojoint.append([i,j])
if len(tojoint):
mix=[]
iDelete = []
for _group in tojoint:
rate = 0.0
rateMax = 0.0
for i in _group:
rate += newpeaks[i][0]
if newpeaks[i][0] > rateMax:
rateMax = newpeaks[i][0]
iMax = i
iDelete += [i]
transition = newpeaksnames[iMax]
ene = 0.0
for i in _group:
ene += newpeaks[i][0] * newpeaks[i][1]/rate
mix.append([ene,rate,transition])
iDelete.sort()
iDelete.reverse()
for i in iDelete:
del newpeaks[i]
del newpeaksnames[i]
output = []
for i in range(len(newpeaks)):
output.append([newpeaks[i][1], newpeaks[i][0], newpeaksnames [i]])
for peak in mix:
output.append(peak)
output.sort()
#intensity threshold
if len(output) <= 1:return output
if ithreshold is not None:
imax = max([x[1] for x in output])
if absoluteithreshold:
threshold = ithreshold
else:
threshold = ithreshold * imax
for i in range(-len(output)+1,1):
if output[i][1] < threshold:
del output[i]
#number threshold
if nthreshold is not None:
if nthreshold < len(output):
div = [[x[1],x] for x in output]
div.sort()
div.reverse()
div = div[:nthreshold]
output = [x[1] for x in div]
output.sort()
#recover original rates
if keeptotalrate:
currenttotal = sum([x[1] for x in output])
if currenttotal > 0:
totalrate = totalrate/currenttotal
output = [[x[0],x[1]*totalrate,x[2]] for x in output]
return output
def _getAttFilteredElementDict(elementsList,
attenuators= None,
detector = None,
funnyfilters = None,
energy = None):
if energy is None: energy = 100.
if attenuators is None:
attenuators = []
if funnyfilters is None:
funnyfilters = []
outputDict = {}
for group in elementsList:
ele = group[1] * 1
if not (ele in outputDict):
outputDict[ele] = {}
outputDict[ele]['rays'] = []
raysforloop = [group[2] + " xrays"]
elementDict = _getUnfilteredElementDict(ele, energy)
for rays in raysforloop:
if rays not in elementDict:continue
else:outputDict[ele]['rays'].append(rays)
outputDict[ele][rays] = []
rates = []
energies = []
transitions = elementDict[rays]
for transition in transitions:
outputDict[ele][rays] += [transition]
outputDict[ele][transition]={}
ene = elementDict[transition]['energy'] * 1
energies += [ene]
rates.append(elementDict[transition]['rate'] * 1.0)
outputDict[ele][transition]['energy'] = ene
#I do not know if to include this loop in the previous one (because rates are 0.0 sometimes)
#attenuators
coeffs = numpy.zeros(len(energies), numpy.float)
for attenuator in attenuators:
formula = attenuator[0]
thickness = attenuator[1] * attenuator[2]
coeffs += thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.zeros(len(energies), numpy.float)
for i in range(len(energies)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
#funnyfilters (only make sense to have more than one if same opening and aligned)
coeffs = numpy.zeros(len(energies), numpy.float)
funnyfactor = None
for attenuator in funnyfilters:
formula = attenuator[0]
thickness = attenuator[1] * attenuator[2]
if funnyfactor is None:
funnyfactor = attenuator[3]
else:
if abs(attenuator[3]-funnyfactor) > 0.0001:
raise ValueError("All funny type filters must have same openning fraction")
coeffs += thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
if funnyfactor is None:
for i in range(len(rates)):
rates[i] *= trans[i]
else:
try:
transFunny = funnyfactor * numpy.exp(-coeffs) +\
(1.0 - funnyfactor)
except OverflowError:
#deal with underflows reported as overflows
transFunny = numpy.zeros(len(energies), numpy.float)
for i in range(len(energies)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in funnyfilters transmission term")
else:
try:
transFunny[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
transFunny = funnyfactor * transFunny + \
(1.0 - funnyfactor)
for i in range(len(rates)):
rates[i] *= (trans[i] * transFunny[i])
#detector term
if detector is not None:
formula = detector[0]
thickness = detector[1] * detector[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = (1.0 - numpy.exp(-coeffs))
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.ones(len(energies), numpy.float)
for i in range(len(energies)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in detector transmission term")
else:
try:
trans[i] = 1.0 - numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
for i in range(len(rates)):
rates[i] *= trans[i]
i = 0
for transition in transitions:
outputDict[ele][transition]['rate'] = rates[i] * 1
i += 1
return outputDict
def getMultilayerFluorescence(multilayer0,
energyList,
layerList = None,
weightList=None,
flagList = None,
fulloutput = None,
beamfilters = None,
elementsList = None,
attenuators = None,
alphain = None,
alphaout = None,
cascade = None,
detector= None,
funnyfilters=None,
forcepresent=None,
secondary=None):
if multilayer0 is None:return []
if secondary is None:secondary=False
if len(multilayer0):
if type(multilayer0[0]) != type([]):
multilayer=[multilayer0 * 1]
else:
multilayer=multilayer0 * 1
if fulloutput is None:fulloutput = 0
if (type(energyList) != type([])) and \
(type(energyList) != numpy.ndarray):
energyList = [energyList]
energyList = numpy.array(energyList, dtype=numpy.float)
if layerList is None:
layerList = list(range(len(multilayer)))
if type(layerList) != type([]):
layerList = [layerList]
if elementsList is not None:
if type(elementsList) != type([]):
elementsList = [elementsList]
if weightList is not None:
if (type(weightList) != type([])) and \
(type(weightList) != numpy.ndarray):
weightList = [weightList]
weightList = numpy.array(weightList, dtype=numpy.float)
else:
weightList = numpy.ones(len(energyList)).astype(numpy.float)
if flagList is not None:
if (type(flagList) != type([])) and \
(type(flagList) != numpy.ndarray):
flagList = [flagList]
flagList = numpy.array(flagList)
else:
flagList = numpy.ones(len(energyList)).astype(numpy.float)
optimized = 0
if beamfilters is None:beamfilters = []
if len(beamfilters):
if type(beamfilters[0]) != type([]):
beamfilters=[beamfilters]
if elementsList is not None:
if len(elementsList):
if type(elementsList[0]) == type([]):
if len(elementsList[0]) == 3:
optimized = 1
if attenuators is None:attenuators = []
if beamfilters is None:beamfilters = []
if alphain is None: alphain = 45.0
if alphaout is None: alphaout = 45.0
if alphain >= 0:
sinAlphaIn = numpy.sin(alphain * numpy.pi / 180.)
else:
sinAlphaIn = numpy.sin(-alphain * numpy.pi / 180.)
sinAlphaOut = numpy.sin(alphaout * numpy.pi / 180.)
origattenuators = attenuators * 1
newbeamfilters = beamfilters * 1
if alphain < 0:
ilayerindexes = list(range(len(multilayer)))
ilayerindexes.reverse()
for ilayer in ilayerindexes:
newbeamfilters.append(multilayer[ilayer] * 1)
newbeamfilters[-1][2] = newbeamfilters[-1][2]/sinAlphaIn
del newbeamfilters[-1]
#normalize incoming beam
i0 = numpy.nonzero(flagList>0)[0]
weightList = numpy.take(weightList, i0).astype(numpy.float)
energyList = numpy.take(energyList, i0).astype(numpy.float)
flagList = numpy.take(flagList, i0).astype(numpy.float)
#normalize selected weights
total = sum(weightList)
if 0:
#old way
for beamfilter in beamfilters:
formula = beamfilter[0]
thickness = beamfilter[1] * beamfilter[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energyList)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
for coef in coeffs:
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
trans = 0.0 * coeffs
weightList = weightList * trans
else:
pass
#new way will be made later
#formula = []
#thickness = []
#for beamfilter in newbeamfilters:
# formula.append(beamfilter[0] * 1)
# thickness.append(beamfilter[1] * beamfilter[2])
#trans = getMaterialTransmission(formula, thickness, energyList,
# density=1.0, thickness = sum(thickness))['transmission']
#weightList = weightList * trans
if total <= 0.0:
raise ValueError("Sum of weights lower or equal to 0")
weightList = weightList / total
#forcepresent is to set concentration 1 for the fit
#useless if elementsList is not given
if forcepresent is None:forcepresent=0
forcedElementsList = []
if elementsList is not None:
if forcepresent:
forcedElementsList = elementsList * 1
keys = []
for ilayer in list(range(len(multilayer))):
pseudomatrix = multilayer[ilayer] * 1
eleDict = getMaterialMassFractions([pseudomatrix[0]], [1.0])
keys += eleDict.keys()
for ele in keys:
todelete = []
for i in list(range(len(forcedElementsList))):
group = forcedElementsList[i]
if optimized: groupElement = group[1] * 1
else: groupElement = group * 1
if ele == groupElement:
todelete.append(i)
todelete.reverse()
for i in todelete:
del forcedElementsList[i]
else:
forcedElementsList = []
#print "forcedElementsList = ",forcedElementsList
#import time
#t0 = time.time()
result = []
dictListList = []
elementsListFinal = []
for ilayer in list(range(len(multilayer))):
dictList = []
if ilayer > 0:
#arrange attenuators
origattenuators.append(multilayer[ilayer-1] * 1)
origattenuators[-1][2] = origattenuators[-1][2]/sinAlphaOut
#arrange beamfilters
if alphain >= 0:
newbeamfilters.append(multilayer[ilayer-1] * 1)
newbeamfilters[-1][2] = newbeamfilters[-1][2]/sinAlphaIn
else:
del newbeamfilters[-1]
if 0:
print(multilayer[ilayer], "beamfilters =", newbeamfilters)
print(multilayer[ilayer], "attenuators =", origattenuators)
if ilayer not in layerList:continue
pseudomatrix = multilayer[ilayer] * 1
newelementsList = []
eleDict = getMaterialMassFractions([pseudomatrix[0]], [1.0])
if eleDict == {}:
raise ValueError("Invalid layer material %s" % pseudomatrix[0])
keys = eleDict.keys()
if elementsList is None:
newelementsList = keys
for key in keys:
if key not in elementsListFinal:
elementsListFinal.append(key)
else:
newelementsList = []
if optimized:
for ele in keys:
for group in elementsList:
if ele == group[1]:
newelementsList.append(group)
else:
for ele in keys:
for group in elementsList:
if ele == group:
newelementsList.append(group)
for group in forcedElementsList:
newelementsList.append(group * 1)
if optimized:
eleDict[group[1] * 1] = {}
eleDict[group[1] * 1] = 1.0
else:
eleDict[group * 1] = {}
eleDict[group * 1] = 1.0
if not len(newelementsList):
dictList.append({})
result.append({})
continue
#here I could recalculate the dictionnary
if optimized:
userElementDict = _getAttFilteredElementDict(newelementsList,
attenuators= origattenuators,
detector = detector,
funnyfilters = funnyfilters,
energy = max(energyList))
workattenuators = None
workdetector = None
workfunnyfilters = None
else:
userElementDict = None
workattenuators = origattenuators * 1
if detector is not None:
workdetector = detector * 1
else:
workdetector = None
if funnyfilters is not None:
workfunnyfilters = funnyfilters * 1
else:
workfunnyfilters = None
newweightlist = numpy.ones(weightList.shape,numpy.float)
if len(newbeamfilters):
coeffs = numpy.zeros(len(energyList), numpy.float)
for beamfilter in newbeamfilters:
formula = beamfilter[0]
thickness = beamfilter[1] * beamfilter[2]
coeffs += thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energyList)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.zeros(len(energyList), numpy.float)
for i in range(len(energyList)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
newweightlist = weightList * trans
else:
newweightlist = weightList * 1
#nobody warrants the list ordered
if optimized:
newelementsListWork = newelementsList * 1
else:
newelementsListWork = [newelementsList * 1]
matrixmutotalexcitation = getMaterialMassAttenuationCoefficients(pseudomatrix[0],
1.0,
energyList)['total']
for justone in newelementsListWork:
if optimized:
if justone[2].upper()[0] == 'K':
shellIdent = 'K'
elif len(justone[2]) == 2:
shellIdent = justone[2].upper()
elif justone[2].upper() == 'L':
shellIdent = 'L3'
elif justone[2].upper() == 'M':
shellIdent = 'M5'
else:
raise ValueError("Unknown Element shell %s" % justone[2])
bindingEnergy = Element[justone[1]]['binding'][shellIdent]
nrgi = numpy.nonzero(energyList >= bindingEnergy)[0]
if len(nrgi) == 0:nrgi=[0]
justoneList = [justone]
matrixmutotalfluorescence = None
if len(nrgi) > 1:
#calculate all the matrix mass attenuation coefficients
#for the fluorescent energies outside the energy loop.
#the energy list could also be taken out of this loop.
element_energies = []
for item in userElementDict[justone[1]][justone[2]+ " xrays"]:
element_energies.append(userElementDict[justone[1]]\
[item]['energy'])
matrixmutotalfluorescence = getMaterialMassAttenuationCoefficients(pseudomatrix[0],
1.0,
element_energies)['total']
else:
matrixmutotalfluorescence = None
else:
justoneList = justone
nrgi = range(len(energyList))
matrixmutotalfluorescence= None
for iene in nrgi:
energy = energyList[iene] * 1.0
#print "before origattenuators = ",origattenuators
dict = getFluorescence(pseudomatrix, energy,
attenuators = workattenuators,
alphain = alphain,
alphaout = alphaout,
#elementsList = newelementsList,
elementsList = justoneList,
cascade = cascade,
detector = workdetector,
funnyfilters = workfunnyfilters,
userElementDict = userElementDict,
matrixmutotalfluorescence=matrixmutotalfluorescence,
matrixmutotalexcitation=matrixmutotalexcitation[iene]*1.0)
#print "after origattenuators = ",origattenuators
if optimized:
#give back with concentration 1
for ele in dict.keys():
dict[ele]['weight'] = newweightlist[iene] * 1.0
dict[ele]['mass fraction'] = eleDict[ele] * 1.0
else:
#already corrected for concentration
for ele in dict.keys():
dict[ele]['weight'] = newweightlist[iene] * eleDict[ele]
dict[ele]['mass fraction'] = eleDict[ele] * 1.0
#if ele == "Cl":print "dict[ele]['mass fraction'] ",eleDict[ele]
dictList.append(dict)
#secondary fluorescence term from next layers
if secondary:
newweightlist2 = newweightlist * 1
for ilayer2 in range(len(multilayer)):
if ilayer2 <= ilayer:continue
#get beam intensity at the layer
pseudomatrix2 = multilayer[ilayer2] * 1
beamfilter = multilayer[ilayer2-1] * 1
formula = beamfilter[0]
thickness = beamfilter[1] * beamfilter[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energyList)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.zeros(len(energyList), numpy.float)
for i in range(len(energyList)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
newweightlist2 = newweightlist2 * trans
#get beam2
for iene in range(len(energyList)):
energy = energyList[iene] * 1.0
escape = getEscape(pseudomatrix2,
energy,
alphain = alphain,
cascade = True,
#up to 20 peaks
nthreshold = 20,
ithreshold = 1.0e-5,
ethreshold = 0.010,
fluorescencemode=True)
if not len(escape):continue
energyList2 = [x[0] for x in escape]
weightList2 = numpy.array([x[1] for x in escape]) * newweightlist2[iene]
#correct for attenuation in intermediate layers!!!
weightList3 = 1.0 * weightList2
for ilayer3 in range(len(multilayer)):
if ilayer3 >= ilayer2:continue
if ilayer3 <= ilayer: continue
#I have an intermediate layer
beamfilter = multilayer[ilayer3] * 1
formula = beamfilter[0]
thickness = beamfilter[1] * beamfilter[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energyList2)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.zeros(len(energyList2), numpy.float)
for i in range(len(energyList2)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
weightList3 = weightList3 * trans
for iene2 in range(len(energyList2)):
energy = energyList2[iene2]
dict2 = getFluorescence(pseudomatrix, energy,
attenuators = workattenuators,
alphain = -90.,
alphaout = alphaout,
elementsList = newelementsList,
cascade = cascade,
detector = workdetector,
funnyfilters = workfunnyfilters,
userElementDict = userElementDict)
if optimized:
#give back with concentration 1
#for ele in dict.keys():
for ele in dict2.keys():
dict2[ele]['weight'] = weightList3[iene2] * 1.0
dict2[ele]['mass fraction'] = eleDict[ele] * 1.0
else:
#already corrected for concentration
#for ele in dict.keys():
for ele in dict2.keys():
dict2[ele]['weight'] = weightList3[iene2] * eleDict[ele]
dict2[ele]['mass fraction'] = eleDict[ele] * 1.0
dictList.append(dict2)
if optimized:
pass
else:
newelementsList = [[getz(x),x] for x in newelementsList]
if fulloutput:
result.append(_combineMatrixFluorescenceDict(dictList, newelementsList))
dictListList += dictList
#print "total elapsed = ",time.time() - t0
if fulloutput:
if optimized:
return [_combineMatrixFluorescenceDict(dictListList, elementsList)] + result
else:
newelementsList = [[getz(x),x] for x in (elementsListFinal + forcedElementsList)]
return [_combineMatrixFluorescenceDict(dictListList, newelementsList)] +result
else:
if optimized:
return _combineMatrixFluorescenceDict(dictListList, elementsList)
else:
newelementsList = [[getz(x),x] for x in (elementsListFinal + forcedElementsList)]
return _combineMatrixFluorescenceDict(dictListList, newelementsList)
def _combineMatrixFluorescenceDict(dictList, elementsList0):
finalDict = {}
elementsList = [[x[0], x[1]] for x in elementsList0]
for z,ele in elementsList:
#print ele
finalDict[ele] = {}
finalDict[ele]['rates'] = {}
finalDict[ele]['mass fraction'] = {}
finalDict[ele]['rays']=[]
for dict in dictList:
if not (ele in dict):continue
if not len(dict[ele]['rays']):continue
finalDict[ele]['mass fraction'] = dict[ele]['mass fraction'] * 1.0
for key in dict[ele]['rates'].keys():
if key not in finalDict[ele]['rates']:
if not ('weight' in dict[ele]):
dict[ele]['weight']=dict['weight'] * 1.0
finalDict[ele]['rates'][key] = dict[ele]['rates'][key] * dict[ele]['weight']
else:
if not ('weight' in dict[ele]):
dict[ele]['weight']=dict['weight'] * 1.0
finalDict[ele]['rates'][key] += dict[ele]['rates'][key] * dict[ele]['weight']
for transitions0 in dict[ele]['rays']:
#try to avoid creation of new references
transitions = transitions0 * 1
if transitions not in dict[ele]['rates'].keys(): continue
if transitions not in finalDict[ele]['rays']:
finalDict[ele]['rays'].append(transitions)
finalDict[ele][transitions] = []
if not (dict[ele]['weight'] > 0.0): continue
else: w = dict[ele]['weight']
for transition0 in dict[ele][transitions]:
transition = transition0 * 1
#print ele,"transition = ",transition
if not (transition in finalDict[ele]):
finalDict[ele][transition] = {'rate':0.0,
'energy':dict[ele][transition]['energy'] * 1}
if transition not in finalDict[ele][transitions]:
finalDict[ele][transitions].append(transition)
if transition not in finalDict[ele].keys():
finalDict[ele][transition] = {'rate':0.0}
if transition in dict[ele]:
if transition in finalDict[ele]:
finalDict[ele][transition]['rate'] += w * dict[ele][transition]['rate']
else:
finalDict[ele][transition] = {}
finalDict[ele][transition]['rate'] = w * dict[ele][transition]['rate']
else:
print(dict[ele][transitions])
print(transition)
print("is this an error?")
sys.exit(0)
return finalDict
def getScattering(matrix, energy, attenuators = None, alphain = None, alphaout = None,
elementsList = None, cascade=None,
detector=None):
if alphain is None: alphain = 45.0
if alphaout is None: alphaout = 45.0
sinAlphaIn = numpy.sin(alphain * (numpy.pi)/180.)
sinAlphaOut = numpy.sin(alphaout * (numpy.pi)/180.)
if attenuators is None: attenuators = []
if len(attenuators):
if type(attenuators[0]) != type([]):
attenuators=[attenuators]
if detector is not None:
if type(detector) != type([]):
raise TypeError("Detector must be a list as [material, density, thickness]")
elif len(detector) != 3:
raise ValueError("Detector must have the form [material, density, thickness]")
if energy is None:
raise ValueError("Invalid Energy")
if elementsList is None:
#get material elements and concentrations
eleDict = getMaterialMassFractions([matrix[0]], [1.0])
if eleDict == {}: return {}
#sort the elements according to atomic number (not needed because the output will be a dictionnary)
keys = eleDict.keys()
elementsList = [[getz(x),x] for x in keys]
elementsList.sort()
else:
if (type(elementsList) != type([])) and (type(elementsList) != types.TupleType):
elementsList = [elementsList]
elementsList = [[getz(x),x] for x in elementsList]
elementsList.sort()
eleDict = {}
for z, ele in elementsList:
eleDict[ele] = 1.0
if energy <= 0.10:
raise ValueError("Invalid Energy %.5g keV" % energy)
#do the job
outputDict = {}
for z,ele in elementsList:
outputDict[ele] ={}
outputDict[ele]['mass fraction'] = eleDict[ele]
outputDict[ele]['rates'] = {}
outputDict[ele]['rays'] = ['Coherent','Compton']
for rays in outputDict[ele]['rays']:
theta = alphain + alphaout
outputDict[ele][rays] = {}
if rays == 'Coherent':
outputDict[ele][rays]['energy'] = energy
rates=[getElementCoherentDifferentialCrossSection(ele, theta, energy)]
else:
outputDict[ele][rays]['energy'] = IncoherentScattering.getComptonScatteringEnergy(energy,
theta)
rates=[getElementComptonDifferentialCrossSection(ele, theta, energy)]
ene = outputDict[ele][rays]['energy']
energies =[ene]
#I do not know if to include this loop in the previous one (because rates are 0.0 sometimes)
#attenuators
for attenuator in attenuators:
formula = attenuator[0]
thickness = attenuator[1] * attenuator[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.zeros(len(energies), numpy.float)
for i in range(len(energies)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
trans = trans
for i in range(len(rates)):
rates[i] *= trans[i]
#detector term
if detector is not None:
formula = detector[0]
thickness = detector[1] * detector[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = (1.0 - numpy.exp(-coeffs))
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.ones(len(rates), numpy.float)
for i in range(len(rates)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
else:
try:
trans[i] = 1.0 - numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
for i in range(len(rates)):
rates[i] *= trans[i]
#matrix term
formula = matrix[0]
thickness = matrix[1] * matrix[2]
energies += [energy]
allcoeffs = getMaterialMassAttenuationCoefficients(formula,1.0,energies)
mutotal = allcoeffs['total']
del energies[-1]
i = 0
if 1:
#thick target term
trans = outputDict[ele]['mass fraction'] * 1.0/(mutotal[-1] + mutotal[i] * (sinAlphaIn/sinAlphaOut))
#correction term
if thickness > 0.0:
if abs(sinAlphaIn) > 0.0:
try:
expterm = numpy.exp(-((mutotal[-1]/sinAlphaIn) +(mutotal[i]/sinAlphaOut)) * thickness)
except OverflowError:
if -((mutotal[-1]/sinAlphaIn) +(mutotal[i]/sinAlphaOut)) * thickness > 0.0:
raise ValueError("Positive exponent in transmission term")
expterm = 0.0
trans *= (1.0 - expterm)
#if ele == 'Pb':
# oldRatio.append(newpeaks[i][0])
# print "energy = %.3f ratio=%.5f transmission = %.5g final=%.5g" % (newpeaks[i][1], newpeaks[i][0],trans,trans * newpeaks[i][0])
rates[i] *= trans
outputDict[ele][rays]['rate'] = rates[i]
outputDict[ele]['rates'][rays] = sum(rates)
#outputDict[ele][rays]= Element[ele]['rays'] * 1
return outputDict
def getFluorescence(matrix, energy, attenuators = None, alphain = None, alphaout = None,
elementsList = None, cascade=None,
detector=None,
funnyfilters=None,
userElementDict=None,
matrixmutotalfluorescence=None,
matrixmutotalexcitation=None):
"""
getFluorescence(matrixlist, energy, attenuators = None, alphain = None, alphaout = None,
elementsList = None, cascade=None, detector=None)
matrixlist is a list of the form [material, density, thickness]
energy is the incident beam energy
attenuators is a list of the form [[material1, density1, thickness1],....]
alphain is the incoming beam angle with sample surface
alphaout is the outgoing beam angle with sample surface
if a given elements list is given, the fluorescence rate will be calculated for ONLY
for those elements without taking into account if they are present in the matrix and
considering a mass fraction of 1 to all of them. This should allow a program to fit
directly concentrations.
cascade is a flag to consider vacancy propagation (it is a crude approximation)
detector is just one attenuator more but treated as (1 - Transmission)
[material, density, thickness]
These formulae are strictly valid only for parallel beams.
Needs to be corrected for detector efficiency (at least solid angle) and incoming intensity.
Secondary transitions are neglected.
"""
if alphain is None: alphain = 45.0
if alphaout is None: alphaout = 45.0
if userElementDict is None:userElementDict = {}
bottomExcitation = False
if (alphain < 0.0) and (alphaout < 0.0):
#it is the same
sinAlphaIn = numpy.sin(-alphain * (numpy.pi)/180.)
sinAlphaOut = numpy.sin(-alphaout * (numpy.pi)/180.)
elif (alphain < 0.0) and (alphaout > 0.0):
#bottom excitation
#print "bottom excitation case"
bottomExcitation = True
sinAlphaIn = numpy.sin(-alphain * (numpy.pi)/180.)
sinAlphaOut = numpy.sin(alphaout * (numpy.pi)/180.)
else:
sinAlphaIn = numpy.sin(alphain * (numpy.pi)/180.)
sinAlphaOut = numpy.sin(alphaout * (numpy.pi)/180.)
if cascade is None:cascade=False
if attenuators is None:
attenuators = []
if len(attenuators):
if type(attenuators[0]) != type([]):
attenuators=[attenuators]
if funnyfilters is None:
funnyfilters = []
if len(funnyfilters):
if type(funnyfilters[0]) != type([]):
funnyfilters=[funnyfilters]
if detector is not None:
if type(detector) != type([]):
raise TypeError(\
"Detector must be a list as [material, density, thickness]")
elif len(detector) != 3:
raise ValueError(\
"Detector must have the form [material, density, thickness]")
if energy is None:
raise ValueError("Invalid Energy")
elementsRays = None
if elementsList is None:
#get material elements and concentrations
eleDict = getMaterialMassFractions([matrix[0]], [1.0])
if eleDict == {}: return {}
#sort the elements according to atomic number
#(not needed because the output will be a dictionnary)
keys = eleDict.keys()
elementsList = [[getz(x),x] for x in keys]
elementsList.sort()
else:
if (type(elementsList) != type([])) and\
(type(elementsList) != types.TupleType):
elementsList = [elementsList]
if len(elementsList[0]) == 3:
raysforloopindex = 0
elementsList.sort()
elementsRays = [x[2] for x in elementsList]
elementsList = [[x[0],x[1]] for x in elementsList]
else:
elementsList = [[getz(x),x] for x in elementsList]
elementsList.sort()
eleDict = {}
for z, ele in elementsList:
eleDict[ele] = 1.0
if energy <= 0.10:
raise ValueError("Invalid Energy %.5g keV" % energy)
#do the job
outputDict = {}
shelllist = ['K', 'L1', 'L2', 'L3','M1', 'M2', 'M3', 'M4', 'M5']
for z,ele in elementsList:
#use own unfiltered dictionnary
if ele in userElementDict:
elementDict = userElementDict[ele]
else:
elementDict = _getUnfilteredElementDict(ele, energy)
if not (ele in outputDict):
outputDict[ele] ={}
outputDict[ele]['mass fraction'] = eleDict[ele]
if not ('rates' in outputDict[ele]):
outputDict[ele]['rates'] = {}
#get the fluorescence term for all shells
fluoWeights = _getFluorescenceWeights(ele, energy, normalize = False,
cascade=cascade)
outputDict[ele]['rays'] = elementDict['rays'] * 1
if elementsRays is None:
raysforloop = elementDict['rays']
else:
if type(elementsRays[raysforloopindex]) != type([]):
raysforloop = [elementsRays[raysforloopindex] + " xrays"]
else:
raysforloop = []
for item in elementsRays[raysforloopindex]:
raysforloop.append(item + " xrays")
raysforloopindex +=1
for rays in raysforloop:
if rays not in elementDict['rays']:continue
outputDict[ele][rays] = []
rates = []
energies = []
transitions = elementDict[rays]
for transition in transitions:
outputDict[ele][rays] += [transition]
outputDict[ele][transition]={}
outputDict[ele][transition]['rate'] = 0.0
if transition[0] == "K":
rates.append(fluoWeights[0] * elementDict[transition]['rate'])
else:
rates.append(fluoWeights[shelllist.index(transition[0:2])] * elementDict[transition]['rate'])
ene = elementDict[transition]['energy']
energies += [ene]
outputDict[ele][transition]['energy'] = ene
#I do not know if to include this loop in the previous one (because rates are 0.0 sometimes)
#attenuators
coeffs = numpy.zeros(len(energies), numpy.float)
for attenuator in attenuators:
formula = attenuator[0]
thickness = attenuator[1] * attenuator[2]
coeffs += thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = numpy.exp(-coeffs)
except OverflowError:
for coef in coeffs:
if coef < 0.0:
raise ValueError("Positive exponent in attenuators transmission term")
trans = 0.0 * coeffs
#funnyfilters
coeffs = numpy.zeros(len(energies), numpy.float)
funnyfactor = None
for attenuator in funnyfilters:
formula = attenuator[0]
thickness = attenuator[1] * attenuator[2]
if funnyfactor is None:
funnyfactor = attenuator[3]
else:
if abs(attenuator[3] - funnyfactor) > 0.0001:
raise ValueError(\
"All funny type filters must have same openning fraction")
coeffs += thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
if funnyfactor is None:
for i in range(len(rates)):
rates[i] *= trans[i]
else:
try:
transFunny = funnyfactor * numpy.exp(-coeffs) +\
(1.0 - funnyfactor)
except OverflowError:
#deal with underflows reported as overflows
transFunny = numpy.zeros(len(energies), numpy.float)
for i in range(len(energies)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError(\
"Positive exponent in funnyfilters transmission term")
else:
try:
transFunny[i] = numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
transFunny = funnyfactor * transFunny + \
(1.0 - funnyfactor)
for i in range(len(rates)):
rates[i] *= (trans[i] * transFunny[i])
#detector term
if detector is not None:
formula = detector[0]
thickness = detector[1] * detector[2]
coeffs = thickness * numpy.array(getMaterialMassAttenuationCoefficients(formula,1.0,energies)['total'])
try:
trans = (1.0 - numpy.exp(-coeffs))
except OverflowError:
#deal with underflows reported as overflows
trans = numpy.ones(len(rates), numpy.float)
for i in range(len(rates)):
coef = coeffs[i]
if coef < 0.0:
raise ValueError(\
"Positive exponent in attenuators transmission term")
else:
try:
trans[i] = 1.0 - numpy.exp(-coef)
except OverflowError:
#if we are here we know it is not an overflow and trans[i] has the proper value
pass
for i in range(len(rates)):
rates[i] *= trans[i]
#matrix term
formula = matrix[0]
thickness = matrix[1] * matrix[2]
energies += [energy]
if matrixmutotalfluorescence is None:
allcoeffs = getMaterialMassAttenuationCoefficients(formula,1.0,energies)
mutotal = allcoeffs['total']
else:
mutotal = matrixmutotalfluorescence * 1
if matrixmutotalexcitation is None:
mutotal.append(getMaterialMassAttenuationCoefficients(formula,
1.0,
energy)['total'][0])
else:
mutotal.append(matrixmutotalexcitation)
#muphoto = allcoeffs['photo']
muphoto = getMaterialMassAttenuationCoefficients(ele,1.0,energy)['photo']
del energies[-1]
i = 0
for transition in transitions:
#thick target term
if rates[i] <= 0.0:trans=0.0
else:
if bottomExcitation:
denominator = (mutotal[-1] - mutotal[i] * (sinAlphaIn/sinAlphaOut))
if denominator == 0.0:
trans = thickness/sinAlphaIn
trans = -outputDict[ele]['mass fraction'] *\
muphoto[-1] * trans *\
numpy.exp(-trans*mutotal[-1])
else:
trans = -outputDict[ele]['mass fraction'] *\
muphoto[-1]/denominator
#correction term
if thickness > 0.0:
try:
expterm = numpy.exp(-(mutotal[-1]/sinAlphaIn) * thickness) -\
numpy.exp(-(mutotal[i]/sinAlphaOut) * thickness)
except OverflowError:
#print "overflow"
if ((-(mutotal[-1]/sinAlphaIn) * thickness) > 0.0) or\
((-(mutotal[i]/sinAlphaOut) * thickness) > 0.0):
raise ValueError("Positive exponent in transmission term")
expterm = 0.0
trans *= expterm
else:
raise ValueError("Incorrect target density and/or thickness")
if trans < 0.0:
print("trans lower than 0.0. Reset to 0.0")
trans = 0.0
else:
trans = outputDict[ele]['mass fraction'] *\
muphoto[-1]/(mutotal[-1] + mutotal[i] * (sinAlphaIn/sinAlphaOut))
#correction term
if thickness > 0.0:
if abs(sinAlphaIn) > 0.0:
try:
expterm = numpy.exp(-((mutotal[-1]/sinAlphaIn) +(mutotal[i]/sinAlphaOut)) * thickness)
except OverflowError:
#print "overflow"
if -((mutotal[-1]/sinAlphaIn) +(mutotal[i]/sinAlphaOut)) * thickness > 0.0:
raise ValueError(\
"Positive exponent in transmission term")
expterm = 0.0
trans *= (1.0 - expterm)
#if ele == 'Pb':
# oldRatio.append(newpeaks[i][0])
# print "energy = %.3f ratio=%.5f transmission = %.5g final=%.5g" % (newpeaks[i][1], newpeaks[i][0],trans,trans * newpeaks[i][0])
rates[i] *= trans
outputDict[ele][transition]['rate'] = rates[i]
i += 1
outputDict[ele]['rates'][rays] = sum(rates)
#outputDict[ele][rays]= Element[ele]['rays'] * 1
return outputDict
def getLWeights(ele,energy=None, normalize = None, shellist = None):
if normalize is None:normalize = True
if shellist is None: shellist = ['L1', 'L2', 'L3']
if type(ele) == type(" "):
pass
else:
ele = getsymbol(int(ele))
if energy is None:
#Use the L shell jumps
w = getLJumpWeight(ele,excitedshells=[1.0,1.0,1.0])
#weights due to Coster Kronig transitions and fluorescence yields
ck= LShell.getCosterKronig(ele)
w[0] = w[0]
w[1] = w[1] + ck['f12'] * w[0]
w[2] = w[2] + ck['f13'] * w[0] + ck['f23'] * w[1]
omega = [ getomegal1(ele), getomegal2(ele), getomegal3(ele)]
for i in range(len(w)):
w[i] *= omega[i]
else:
#Take into account the cascade as in the getFluorescence method
#The PyMCA fit was already using that when there was a matrix but
#it was not shown in the Elements Info window.
allweights = _getFluorescenceWeights(ele, energy, normalize = False, cascade = True)
w = allweights[1:4]
if normalize:
cum = sum(w)
if cum > 0.0:
for i in range(len(w)):
w[i] /= cum
return w
def getMWeights(ele,energy=None, normalize = None, shellist = None):
if normalize is None:normalize = True
if shellist is None: shellist = ['M1', 'M2', 'M3', 'M4', 'M5']
if type(ele) == type(" "):
pass
else:
ele = getsymbol(int(ele))
if energy is None:
w = getMJumpWeight(ele,excitedshells=[1.0,1.0,1.0,1.0,1.0])
#weights due to Coster Kronig transitions and fluorescence yields
ck= MShell.getCosterKronig(ele)
w[0] = w[0]
w[1] = w[1] + ck['f12'] * w[0]
w[2] = w[2] + ck['f13'] * w[0] + ck['f23'] * w[1]
w[3] = w[3] + ck['f14'] * w[0] + ck['f24'] * w[1] + ck['f34'] * w[2]
w[4] = w[4] + ck['f15'] * w[0] + ck['f25'] * w[1] + ck['f35'] * w[2] + ck['f45'] * w[3]
omega = [ getomegam1(ele), getomegam2(ele), getomegam3(ele), getomegam4(ele), getomegam5(ele)]
for i in range(len(w)):
w[i] *= omega[i]
else:
#Take into account the cascade as in the getFluorescence method
#The PyMCA fit was already using that when there was a matrix but
#it was not shown in the Elements Info window.
allweights = _getFluorescenceWeights(ele, energy, normalize = False, cascade = True)
w = allweights[4:9]
if normalize:
cum = sum(w)
for i in range(len(w)):
if cum > 0.0:
w[i] /= cum
return w
def getxrayenergy(symbol,transition):
if len(symbol) > 1:
ele = symbol[0].upper() + symbol[1].lower()
else:
ele = symbol.upper()
trans = transition.upper()
z = getz(ele)
if z > len(ElementBinding):
#Give the bindings of the last element
energies = ElementBinding[-1]
else:
energies = ElementBinding[z-1]
if len(trans) == 2:
trans=trans[0:2]+'2'
if trans[0:1] == 'K':
i=1
emax = energies[ElementShells.index('K')+1]
elif trans[0:2] in ElementShells:
i=2
emax = energies[ElementShells.index(trans[0:2])+1]
else:
#print transition
#print "Shell %s not in Element %s Shells" % (trans[0:2], ele)
return -1
if trans[i:i+2] in ElementShells:
emin = energies[ElementShells.index(trans[i:i+2])+1]
else:
if (z > 80) and (trans[i:i+2] == "Q1"):
emin = 0.003
else:
#print "HERE ",trans[i:i+2],transition,z
#print "Final shell %s not in Element %s Shells" % (trans[i:i+1], ele)
return -1
if emin > emax:
if z != 13:
print("Warning, negative energy!")
print("Please report this message:")
print("Symbol=",symbol)
print("emin = ",emin)
print("emax = ",emax)
print("z = ",z)
print("transition = ",transition)
print("the transition will be ignored")
return emax - emin
def isValidFormula(compound):
#Avoid Fe 2 or Fe-2 or SRM-1832 being considered as valid formulae
for c in [" ", "-", "_"]:
if c in compound:
return False
#single element case
if compound in Element.keys():return True
try:
elts= [ w for w in re.split('[0-9]', compound) if w != '' ]
nbs= [ int(w) for w in re.split('[a-zA-Z]', compound) if w != '' ]
except:
return False
if len(elts)==1 and len(nbs)==0:
if type(elts) == type([]):
return False
if elts in Element.keys():
return True
else:
return False
if (len(elts)==0 and len(nbs)==0) or (len(elts) != len(nbs)):return False
return True
def isValidMaterial(compound):
if compound in Material.keys():return True
elif isValidFormula(compound):return True
else:return False
def getMaterialKey(compound):
matkeys = Material.keys()
if compound in matkeys:return compound
compoundHigh = compound.upper()
matkeysHigh = []
for key in matkeys:
matkeysHigh.append(key.upper())
if compoundHigh in matkeysHigh:
index = matkeysHigh.index(compoundHigh)
return matkeys[index]
return None
def getmassattcoef(compound, energy=None):
"""
Usage: getmassattcoef(element symbol/composite, energy in kev)
Computes mass attenuation coefficients for a single element or a compound.
It gets the info from files generated by XCOM
If energy is not given, it gives back a dictionary with the form:
dict['energy'] = [energies]
dict['coherent'] = [coherent scattering cross section(energies)]
dict['compton'] = [incoherent scattering cross section(energies)]
dict['photo'] = [photoelectic effect cross section(energies)]
dict['pair'] = [pair production cross section(energies)]
dict['total'] = [total cross section]
A compound is defined with a string as follow:
'C22H10N2O5' means 22 * C, 10 * H, 2 * N, 5 * O
xsection = SUM(xsection(zi)*ni*ai) / SUM(ai*ni)
zi = Z of each element
ni = number of element zi
ai = atomic weight of element zi
Result in cm2/g
"""
#single element case
if compound in Element.keys():
return getelementmassattcoef(compound,energy)
elts= [ w for w in re.split('[0-9]', compound) if w != '' ]
nbs= [ int(w) for w in re.split('[a-zA-Z]', compound) if w != '' ]
if len(elts)==1 and len(nbs)==0:
if elts in Element.keys():
return getelementmassattcoef(compound,energy)
else:
return {}
if (len(elts)==0 and len(nbs)==0) or (len(elts) != len(nbs)):
return {}
fraction = [Element[elt]['mass'] *nb for (elt, nb) in zip(elts, nbs) ]
div = sum(fraction)
fraction = [x/div for x in fraction]
#print "fraction = ",fraction
ddict={}
ddict['energy'] = []
ddict['coherent'] = []
ddict['compton'] = []
ddict['photo'] = []
ddict['pair'] = []
ddict['total'] = []
eltindex = 0
if energy is None:
energy=[]
for ele in elts:
xcom_data = getelementmassattcoef(ele,None)['energy']
for ene in xcom_data:
if ene not in energy:
energy.append(ene)
energy.sort()
for ele in elts:
xcom_data = getelementmassattcoef(ele,None)
#now I have to interpolate at the different energies
if not hasattr(energy, "__len__"):
energy =[energy]
eneindex = 0
for ene in energy:
if ene < 1.0:
if PyMcaEPDL97.EPDL97_DICT[ele]['original']:
#make sure the binding energies are those used by this module and not EADL ones
PyMcaEPDL97.setElementBindingEnergies(ele,
Element[ele]['binding'])
tmpDict = PyMcaEPDL97.getElementCrossSections(ele, ene)
cohe = tmpDict['coherent'][0]
comp = tmpDict['compton'][0]
photo = tmpDict['photo'][0]
pair = 0.0
else:
i0=max(numpy.nonzero(xcom_data['energy'] <= ene)[0])
i1=min(numpy.nonzero(xcom_data['energy'] >= ene)[0])
if (i1 == i0) or (i0>i1):
cohe=xcom_data['coherent'][i1]
comp=xcom_data['compton'][i1]
photo=xcom_data['photo'][i1]
pair=xcom_data['pair'][i1]
else:
if LOGLOG:
A=xcom_data['energylog10'][i0]
B=xcom_data['energylog10'][i1]
logene = numpy.log10(ene)
c2=(logene-A)/(B-A)
c1=(B-logene)/(B-A)
else:
A=xcom_data['energy'][i0]
B=xcom_data['energy'][i1]
c2=(ene-A)/(B-A)
c1=(B-ene)/(B-A)
cohe= pow(10.0,c2*xcom_data['coherentlog10'][i1]+\
c1*xcom_data['coherentlog10'][i0])
comp= pow(10.0,c2*xcom_data['comptonlog10'][i1]+\
c1*xcom_data['comptonlog10'][i0])
photo=pow(10.0,c2*xcom_data['photolog10'][i1]+\
c1*xcom_data['photolog10'][i0])
if xcom_data['pair'][i1] > 0.0:
c2 = c2*numpy.log10(xcom_data['pair'][i1])
if xcom_data['pair'][i0] > 0.0:
c1 = c1*numpy.log10(xcom_data['pair'][i0])
pair = pow(10.0,c1+c2)
else:
pair =0.0
else:
pair =0.0
if eltindex == 0:
ddict['energy'].append(ene)
ddict['coherent'].append(cohe *fraction[eltindex])
ddict['compton'].append(comp *fraction[eltindex])
ddict['photo'].append(photo *fraction[eltindex])
ddict['pair'].append(pair*fraction[eltindex])
ddict['total'].append((cohe+comp+photo+pair)*fraction[eltindex])
else:
ddict['coherent'][eneindex] += cohe *fraction[eltindex]
ddict['compton'] [eneindex] += comp *fraction[eltindex]
ddict['photo'] [eneindex] += photo *fraction[eltindex]
ddict['pair'] [eneindex] += pair *fraction[eltindex]
ddict['total'] [eneindex] += (cohe+comp+photo+pair) * fraction[eltindex]
eneindex += 1
eltindex += 1
return ddict
def __materialInCompoundList(lst):
for item in lst:
if item in Material.keys():
return True
return False
def getMaterialTransmission(compoundList0, fractionList0, energy0 = None,
density=None, thickness=None, listoutput=True):
"""
Usage:
getMaterialTransmission(compoundList, fractionList, energy = None,
density=None, thickness=None):
Input
compoundlist - List of elements, compounds or materials
fractionlist - List of floats indicating the amount of respective material
energy - Photon energy (it can be a list)
density - Density in g/cm3 (default is 1.0)
thickness - Thickness in cm (default is 1.0)
The product density * thickness has to be in g/cm2
Output
Detailed dictionary.
"""
if density is None: density = 1.0
if thickness is None: thickness = 1.0
dict = getMaterialMassAttenuationCoefficients(compoundList0,
fractionList0, energy0)
energy = numpy.array(dict['energy'],numpy.float)
mu = numpy.array(dict['total'],numpy.float) * density * thickness
if energy0 is not None:
if type(energy0) != type([]):
listoutput = False
if listoutput:
dict['energy'] = energy.tolist()
dict['density'] = density
dict['thickness'] = thickness
dict['transmission'] = numpy.exp(-mu).tolist()
else:
dict['energy'] = energy
dict['density'] = density
dict['thickness'] = thickness
dict['transmission'] = numpy.exp(-mu)
return dict
def getMaterialMassFractions(compoundList0, fractionList0):
return getMaterialMassAttenuationCoefficients(compoundList0, fractionList0, None, massfractions=True)
def getMaterialMassAttenuationCoefficients(compoundList0, fractionList0, energy0 = None,massfractions=False):
"""
Usage:
getMaterialMassAttenuationCoefficients(compoundList, fractionList,
energy = None,massfractions=False)
compoundList - List of compounds into the material
fractionList - List of masses of each compound
energy - Energy at which the values are desired
massfractions- Flag to supply mass fractions on output
"""
if type(compoundList0) != type([]):
compoundList = [compoundList0]
else:
compoundList = compoundList0
if type(fractionList0) == numpy.ndarray:
fractionList = fractionList0.tolist()
elif type(fractionList0) != type([]):
fractionList = [fractionList0]
else:
fractionList = fractionList0
fractionList = [float(x) for x in fractionList]
while __materialInCompoundList(compoundList):
total=sum(fractionList)
compoundFractionList = [x/total for x in fractionList]
#allow materials in compoundList
newcompound = []
newfraction = []
deleteitems = []
for compound in compoundList:
if compound in Material.keys():
if type(Material[compound]['CompoundList']) != type([]):
Material[compound]['CompoundList']=[Material[compound]['CompoundList']]
if type(Material[compound]['CompoundFraction']) != type([]):
Material[compound]['CompoundFraction']=[Material[compound]['CompoundFraction']]
Material[compound]['CompoundFraction'] = [float(x) for x in Material[compound]['CompoundFraction']]
total = sum(Material[compound]['CompoundFraction'])
j = compoundList.index(compound)
compoundfraction = fractionList[j]
i = 0
for item in Material[compound]['CompoundList']:
newcompound.append(item)
newfraction.append(Material[compound]['CompoundFraction'][i] * compoundfraction /total)
i += 1
deleteitems.append(j)
if len(deleteitems):
deleteitems.reverse()
for i in deleteitems:
del compoundList[i]
del fractionList[i]
for i in range(len(newcompound)):
compoundList.append(newcompound[i])
fractionList.append(newfraction[i])
total=sum(fractionList)
compoundFractionList = [float(x)/total for x in fractionList]
materialElements = {}
energy = energy0
if energy0 is not None:
if type(energy0) == type(2.):
energy = [energy0]
elif type(energy0) == type(1):
energy = [1.0 * energy0]
elif type(energy0) == numpy.ndarray:
energy = energy0.tolist()
for compound in compoundList:
elts=[]
#get energy list
if compound in Element.keys():
elts=[compound]
nbs =[1]
else:
elts= [ w for w in re.split('[0-9]', compound) if w != '' ]
try:
nbs= [ int(w) for w in re.split('[a-zA-Z]', compound) if w != '' ]
except:
raise ValueError("Compound '%s' not understood" % compound)
if len(elts)==1 and len(nbs)==0:
elts=[compound]
nbs =[1]
if (len(elts)==0 and len(nbs)==0) or (len(elts) != len(nbs)):
print("compound %s not understood" % compound)
raise ValueError("compound %s not understood" % compound)
#the proportion of the element in that compound times the compound fraction
fraction = [Element[elt]['mass'] *nb for (elt, nb) in zip(elts, nbs) ]
div = sum(fraction)/compoundFractionList[compoundList.index(compound)]
fraction = [x/div for x in fraction]
if energy is None:
#get energy list
energy = []
for ele in elts:
xcom_data = getelementmassattcoef(ele,None)['energy']
for ene in xcom_data:
if ene not in energy:
energy.append(ene)
for ele in elts:
if ele not in materialElements.keys():
materialElements[ele] = fraction[elts.index(ele)]
else:
materialElements[ele] += fraction[elts.index(ele)]
if massfractions == True:
return materialElements
if energy0 is None:
energy.sort()
#I have the energy grid, the elements and their fractions
dict={}
dict['energy'] = []
dict['coherent'] = []
dict['compton'] = []
dict['photo'] = []
dict['pair'] = []
dict['total'] = []
eltindex = 0
for ele in materialElements.keys():
if 'xcom' in Element[ele]:
xcom_data = Element[ele]['xcom']
else:
xcom_data = getelementmassattcoef(ele,None)
#now I have to interpolate at the different energies
if (type(energy) != type([])):
energy =[energy]
eneindex = 0
for ene in energy:
if ene < 1.0:
if PyMcaEPDL97.EPDL97_DICT[ele]['original']:
#make sure the binding energies are those used by this module and not EADL ones
PyMcaEPDL97.setElementBindingEnergies(ele,
Element[ele]['binding'])
tmpDict = PyMcaEPDL97.getElementCrossSections(ele, ene)
cohe = tmpDict['coherent'][0]
comp = tmpDict['compton'][0]
photo = tmpDict['photo'][0]
pair = 0.0
else:
i0=max(numpy.nonzero(xcom_data['energy'] <= ene)[0])
i1=min(numpy.nonzero(xcom_data['energy'] >= ene)[0])
if (i1 == i0) or (i0>i1):
cohe=xcom_data['coherent'][i1]
comp=xcom_data['compton'][i1]
photo=xcom_data['photo'][i1]
pair=xcom_data['pair'][i1]
else:
if LOGLOG:
A=xcom_data['energylog10'][i0]
B=xcom_data['energylog10'][i1]
logene = numpy.log10(ene)
c2=(logene-A)/(B-A)
c1=(B-logene)/(B-A)
else:
A=xcom_data['energy'][i0]
B=xcom_data['energy'][i1]
c2=(ene-A)/(B-A)
c1=(B-ene)/(B-A)
cohe= pow(10.0,c2*xcom_data['coherentlog10'][i1]+\
c1*xcom_data['coherentlog10'][i0])
comp= pow(10.0,c2*xcom_data['comptonlog10'][i1]+\
c1*xcom_data['comptonlog10'][i0])
photo=pow(10.0,c2*xcom_data['photolog10'][i1]+\
c1*xcom_data['photolog10'][i0])
if xcom_data['pair'][i1] > 0.0:
c2 = c2*numpy.log10(xcom_data['pair'][i1])
if xcom_data['pair'][i0] > 0.0:
c1 = c1*numpy.log10(xcom_data['pair'][i0])
pair = pow(10.0,c1+c2)
else:
pair =0.0
else:
pair =0.0
if eltindex == 0:
dict['energy'].append(ene)
dict['coherent'].append(cohe * materialElements[ele])
dict['compton'].append(comp * materialElements[ele])
dict['photo'].append(photo * materialElements[ele])
dict['pair'].append(pair* materialElements[ele])
dict['total'].append((cohe+comp+photo+pair)* materialElements[ele])
else:
dict['coherent'][eneindex] += cohe * materialElements[ele]
dict['compton'] [eneindex] += comp * materialElements[ele]
dict['photo'] [eneindex] += photo * materialElements[ele]
dict['pair'] [eneindex] += pair * materialElements[ele]
dict['total'] [eneindex] += (cohe+comp+photo+pair) * materialElements[ele]
eneindex += 1
eltindex += 1
return dict
def getcandidates(energy,threshold=None,targetrays=None):
if threshold is None:
threshold = 0.010
if targetrays is None:
targetrays=['K', 'L1', 'L2', 'L3', 'M']
if type(energy) != type([]):
energy = [energy]
if type(targetrays) != type([]):
targetrays = [targetrays]
#K lines
lines ={}
index = 0
for ene in energy:
lines[index] = {'energy':ene,
'elements':[]}
for ele in ElementList:
for ray in targetrays:
rays = ray + " xrays"
if 'rays' in Element[ele]:
for transition in Element[ele][rays]:
e = Element[ele][transition]['energy']
r = Element[ele][transition]['rate']
if abs(ene-e) < threshold:
if ele not in lines[index]['elements']:
lines[index]['elements'].append(ele)
lines[index][ele]=[]
lines[index][ele].append([transition, e, r])
index += 1
return lines
def getElementFormFactor(ele, theta, energy):
if ele in CoherentScattering.COEFFICIENTS.keys():
return CoherentScattering.getElementFormFactor(ele, theta, energy)
else:
try:
z = int(ele)
ele = getsymbol(z)
return CoherentScattering.getElementFormFactor(ele, theta, energy)
except:
raise ValueError("Unknown element %s" % ele)
def getElementCoherentDifferentialCrossSection(ele, theta, energy, p1=None):
#if ele in CoherentScattering.COEFFICIENTS.keys():
if ele in ElementList:
value=CoherentScattering.\
getElementCoherentDifferentialCrossSection(ele, theta, energy, p1)
else:
try:
z = int(ele)
ele = getsymbol(z)
value=CoherentScattering.\
getElementCoherentDifferentialCrossSection(ele, theta, energy, p1)
except:
raise ValueError("Unknown element %s" % ele)
#convert from cm2/atom to cm2/g
return (value * AVOGADRO_NUMBER)/ Element[ele]['mass']
def getElementIncoherentScatteringFunction(ele, theta, energy):
if ele in ElementList:
value = IncoherentScattering.\
getElementIncoherentScatteringFunction(ele, theta, energy)
else:
try:
z = int(ele)
ele = getsymbol(z)
value = IncoherentScattering.\
getElementIncoherentScatteringFunction(ele, theta, energy)
except:
raise ValueError("Unknown element %s" % ele)
return value
def getElementComptonDifferentialCrossSection(ele, theta, energy, p1=None):
if ele in ElementList:
value = IncoherentScattering.\
getElementComptonDifferentialCrossSection(ele, theta, energy, p1)
else:
try:
z = int(ele)
ele = getsymbol(z)
value = IncoherentScattering.\
getElementComptonDifferentialCrossSection(ele, theta, energy, p1)
except:
raise ValueError("Unknown element %s" % ele)
return (value * 6.022142E23)/ Element[ele]['mass']
def getelementmassattcoef(ele,energy=None):
"""
Usage: getelementmassattcoef(element symbol, energy in kev)
It gets the info from files generated by XCOM
If energy is not given, it gives back a dictionary with the form:
dict['energy'] = [energies]
dict['coherent'] = [coherent scattering cross section(energies)]
dict['compton'] = [incoherent scattering cross section(energies)]
dict['photo'] = [photoelectic effect cross section(energies)]
dict['pair'] = [pair production cross section(energies)]
dict['total'] = [total cross section]
"""
if 'xcom' not in Element[ele].keys():
dirmod = PyMcaDataDir.PYMCA_DATA_DIR
#read xcom file
#print dirmod+"/"+ele+".mat"
xcomfile = os.path.join(dirmod, "attdata")
xcomfile = os.path.join(xcomfile, ele+".mat")
if not os.path.exists(xcomfile):
#freeze does bad things with the path ...
dirmod = os.path.dirname(dirmod)
xcomfile = os.path.join(dirmod, "attdata")
xcomfile = os.path.join(xcomfile, ele+".mat")
if dirmod.lower().endswith(".zip"):
dirmod = os.path.dirname(dirmod)
xcomfile = os.path.join(dirmod, "attdata")
xcomfile = os.path.join(xcomfile, ele+".mat")
if not os.path.exists(xcomfile):
print("Cannot find file ",xcomfile)
raise IOError("Cannot find %s" % xcomfile)
f = open(xcomfile, 'r')
line=f.readline()
while (line.split('ENERGY')[0] == line):
line = f.readline()
Element[ele]['xcom'] = {}
Element[ele]['xcom']['energy'] =[]
Element[ele]['xcom']['coherent'] =[]
Element[ele]['xcom']['compton'] =[]
Element[ele]['xcom']['photo'] =[]
Element[ele]['xcom']['pair'] =[]
Element[ele]['xcom']['total'] =[]
line = f.readline()
while (line.split('COHERENT')[0] == line):
line = line.split()
for value in line:
Element[ele]['xcom']['energy'].append(float(value)*1000.)
line = f.readline()
Element[ele]['xcom']['energy']=numpy.array(Element[ele]['xcom']['energy'])
line = f.readline()
while (line.split('INCOHERENT')[0] == line):
line = line.split()
for value in line:
Element[ele]['xcom']['coherent'].append(float(value))
line = f.readline()
Element[ele]['xcom']['coherent']=numpy.array(Element[ele]['xcom']['coherent'])
line = f.readline()
while (line.split('PHOTO')[0] == line):
line = line.split()
for value in line:
Element[ele]['xcom']['compton'].append(float(value))
line = f.readline()
Element[ele]['xcom']['compton']=numpy.array(Element[ele]['xcom']['compton'])
line = f.readline()
while (line.split('PAIR')[0] == line):
line = line.split()
for value in line:
Element[ele]['xcom']['photo'].append(float(value))
line = f.readline()
line = f.readline()
while (line.split('PAIR')[0] == line):
line = line.split()
for value in line:
Element[ele]['xcom']['pair'].append(float(value))
line = f.readline()
i = 0
line = f.readline()
while (len(line)):
line = line.split()
for value in line:
Element[ele]['xcom']['pair'][i] += float(value)
i += 1
line = f.readline()
if sys.version >= '3.0':
# next line gave problems under under windows
# just try numpy.argsort([1,1,1,1,1]) under linux and windows to see
# what I mean
# i1=numpy.argsort(Element[ele]['xcom']['energy']) did not work
# (uses quicksort and gives problems with Pb not passing tests)
i1=numpy.argsort(Element[ele]['xcom']['energy'], kind='mergesort')
else:
sset = map(None,Element[ele]['xcom']['energy'],range(len(Element[ele]['xcom']['energy'])))
sset.sort()
i1=numpy.array([x[1] for x in sset])
Element[ele]['xcom']['energy']=numpy.take(Element[ele]['xcom']['energy'],i1)
Element[ele]['xcom']['coherent']=numpy.take(Element[ele]['xcom']['coherent'],i1)
Element[ele]['xcom']['compton']=numpy.take(Element[ele]['xcom']['compton'],i1)
Element[ele]['xcom']['photo']=numpy.take(Element[ele]['xcom']['photo'],i1)
Element[ele]['xcom']['pair']=numpy.take(Element[ele]['xcom']['pair'],i1)
if Element[ele]['xcom']['coherent'][0] <= 0:
Element[ele]['xcom']['coherent'][0] = Element[ele]['xcom']['coherent'][1] * 1.0
try:
Element[ele]['xcom']['energylog10']=numpy.log10(Element[ele]['xcom']['energy'])
Element[ele]['xcom']['coherentlog10']=numpy.log10(Element[ele]['xcom']['coherent'])
Element[ele]['xcom']['comptonlog10']=numpy.log10(Element[ele]['xcom']['compton'])
Element[ele]['xcom']['photolog10']=numpy.log10(Element[ele]['xcom']['photo'])
except:
raise ValueError("Problem calculating logaritm of %s.mat file data" % ele)
for i in range(0,len(Element[ele]['xcom']['energy'])):
Element[ele]['xcom']['total'].append(Element[ele]['xcom']['coherent'][i]+\
Element[ele]['xcom']['compton'] [i]+\
Element[ele]['xcom']['photo'] [i]+\
Element[ele]['xcom']['pair'] [i])
if energy is None:
return Element[ele]['xcom']
ddict={}
ddict['energy'] = []
ddict['coherent'] = []
ddict['compton'] = []
ddict['photo'] = []
ddict['pair'] = []
ddict['total'] = []
if not hasattr(energy, "__len__"):
energy =[energy]
for ene in energy:
if ene < 1.0:
if PyMcaEPDL97.EPDL97_DICT[ele]['original']:
#make sure the binding energies are those used by this module and not EADL ones
PyMcaEPDL97.setElementBindingEnergies(ele,
Element[ele]['binding'])
tmpDict = PyMcaEPDL97.getElementCrossSections(ele, ene)
cohe = tmpDict['coherent'][0]
comp = tmpDict['compton'][0]
photo = tmpDict['photo'][0]
pair = 0.0
else:
i0=max(numpy.nonzero(Element[ele]['xcom']['energy'] <= ene)[0])
i1=min(numpy.nonzero(Element[ele]['xcom']['energy'] >= ene)[0])
if i1 <= i0:
cohe=Element[ele]['xcom']['coherent'][i1]
comp=Element[ele]['xcom']['compton'][i1]
photo=Element[ele]['xcom']['photo'][i1]
pair=Element[ele]['xcom']['pair'][i1]
else:
if LOGLOG:
A=Element[ele]['xcom']['energylog10'][i0]
B=Element[ele]['xcom']['energylog10'][i1]
logene = numpy.log10(ene)
c2=(logene-A)/(B-A)
c1=(B-logene)/(B-A)
else:
A=Element[ele]['xcom']['energy'][i0]
B=Element[ele]['xcom']['energy'][i1]
c2=(ene-A)/(B-A)
c1=(B-ene)/(B-A)
cohe= pow(10.0,c2*Element[ele]['xcom']['coherentlog10'][i1]+\
c1*Element[ele]['xcom']['coherentlog10'][i0])
comp= pow(10.0,c2*Element[ele]['xcom']['comptonlog10'][i1]+\
c1*Element[ele]['xcom']['comptonlog10'][i0])
photo=pow(10.0,c2*Element[ele]['xcom']['photolog10'][i1]+\
c1*Element[ele]['xcom']['photolog10'][i0])
if Element[ele]['xcom']['pair'][i1] > 0.0:
c2 = c2*numpy.log10(Element[ele]['xcom']['pair'][i1])
if Element[ele]['xcom']['pair'][i0] > 0.0:
c1 = c1*numpy.log10(Element[ele]['xcom']['pair'][i0])
pair = pow(10.0,c1+c2)
else:
pair =0.0
else:
pair =0.0
ddict['energy'].append(ene)
ddict['coherent'].append(cohe)
ddict['compton'].append(comp)
ddict['photo'].append(photo)
ddict['pair'].append(pair)
ddict['total'].append(cohe+comp+photo+pair)
return ddict
def getElementLShellRates(symbol,energy=None,photoweights = None):
"""
getElementLShellRates(symbol,energy=None, photoweights = None)
gives LShell branching ratios at a given energy
weights due to photoeffect, fluorescence and Coster-Kronig
transitions are calculated and used unless photoweights is False,
in that case weights = [1.0, 1.0, 1.0, 1.0, 1.0]
"""
if photoweights is None:photoweights=True
if photoweights:
weights = getLWeights(symbol,energy=energy)
else:
weights = [1.0, 1.0, 1.0]
z = getz(symbol)
index = z-1
shellrates = numpy.arange(len(LShell.ElementLShellTransitions)).astype(numpy.float)
shellrates[0] = z
shellrates[1] = 0
lo = 0
if 'Z' in LShell.ElementL1ShellTransitions[0:2]:lo=1
if 'TOTAL' in LShell.ElementL1ShellTransitions[0:2]:lo=lo+1
n1 = len(LShell.ElementL1ShellTransitions)
rates = numpy.array(LShell.ElementL1ShellRates[index]).astype(numpy.float)
shellrates[lo:n1] = (rates[lo:] / (sum(rates[lo:]) + (sum(rates[lo:])==0))) * weights[0]
n2 = n1 + len(LShell.ElementL2ShellTransitions) - lo
rates = numpy.array(LShell.ElementL2ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[lo:] / (sum(rates[lo:]) + (sum(rates[lo:])==0))) * weights[1]
n1 = n2
n2 = n1 + len(LShell.ElementL3ShellTransitions) - lo
rates = numpy.array(LShell.ElementL3ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[lo:] / (sum(rates[lo:]) + (sum(rates[lo:])==0))) * weights[2]
return shellrates
def getElementMShellRates(symbol,energy=None, photoweights = None):
"""
getElementMShellRates(symbol,energy=None, photoweights = None)
gives MShell branching ratios at a given energy
weights due to photoeffect, fluorescence and Coster-Kronig
transitions are calculated and used unless photoweights is False,
in that case weights = [1.0, 1.0, 1.0, 1.0, 1.0]
"""
if photoweights is None:photoweights=True
if photoweights:
weights = getMWeights(symbol,energy=energy)
else:
weights = [1.0, 1.0, 1.0, 1.0, 1.0]
z = getz(symbol)
index = z-1
shellrates = numpy.arange(len(MShell.ElementMShellTransitions)).astype(numpy.float)
shellrates[0] = z
shellrates[1] = 0
n1 = len(MShell.ElementM1ShellTransitions)
rates = numpy.array(MShell.ElementM1ShellRates[index]).astype(numpy.float)
shellrates[2:n1] = (rates[2:] / (sum(rates[2:]) + (sum(rates[2:])==0))) * weights[0]
n2 = n1 + len(MShell.ElementM2ShellTransitions) - 2
rates = numpy.array(MShell.ElementM2ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[2:] / (sum(rates[2:]) + (sum(rates[2:])==0))) * weights[1]
n1 = n2
n2 = n1 + len(MShell.ElementM3ShellTransitions) - 2
rates = numpy.array(MShell.ElementM3ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[2:] / (sum(rates[2:]) + (sum(rates[2:])==0))) * weights[2]
n1 = n2
n2 = n1 + len(MShell.ElementM4ShellTransitions) - 2
rates = numpy.array(MShell.ElementM4ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[2:] / (sum(rates[2:]) + (sum(rates[2:])==0)))* weights[3]
n1 = n2
n2 = n1 + len(MShell.ElementM5ShellTransitions) - 2
rates = numpy.array(MShell.ElementM5ShellRates[index]).astype(numpy.float)
shellrates[n1:n2] = (rates[2:] / (sum(rates[2:]) + (sum(rates[2:])==0)))* weights[4]
return shellrates
def _getUnfilteredElementDict(symbol, energy, photoweights=None):
if photoweights == None:photoweights = False
ddict = {}
if len(symbol) > 1:
ele = symbol[0].upper() + symbol[1].lower()
else:
ele = symbol.upper()
#fill the dictionnary
ddict['rays']=[]
z = getz(ele)
for n in range(len(ElementXrays)):
rays = ElementXrays[n]
if (rays == 'L xrays'):
shellrates = getElementLShellRates(ele,energy=energy,photoweights=photoweights)
elif (rays == 'M xrays'):
shellrates = getElementMShellRates(ele,energy=energy,photoweights=photoweights)
else:
shellrates = ElementShellRates[n][z-1]
shelltransitions = ElementShellTransitions[n]
ddict[rays] = []
minenergy = MINENERGY
if 'TOTAL' in shelltransitions:
indexoffset = 2
else:
indexoffset = 1
for i in range(indexoffset, len(shelltransitions)):
rate = shellrates [i]
transition = shelltransitions[i]
if n==0:ddict[transition] = {}
if (rays == "Ka xrays"):
xenergy = getxrayenergy(ele,transition.replace('a',''))
elif (rays == "Kb xrays"):
xenergy = getxrayenergy(ele,transition.replace('b',''))
else:
xenergy = getxrayenergy(ele,transition.replace('*',''))
if xenergy > minenergy:
ddict[transition] = {}
ddict[rays].append(transition)
ddict[transition]['energy'] = xenergy
ddict[transition]['rate'] = rate
if rays not in ddict['rays']:
ddict['rays'].append(rays)
ddict['buildparameters']={}
ddict['buildparameters']['energy'] = energy
ddict['buildparameters']['minenergy'] = minenergy
ddict['buildparameters']['minrate'] = 0.0
return ddict
def _updateElementDict(symbol, dict, energy=None, minenergy=MINENERGY, minrate=0.0010,
normalize = None, photoweights = None):
if normalize is None: normalize = True
if photoweights is None: photoweights = True
if len(symbol) > 1:
ele = symbol[0].upper() + symbol[1].lower()
else:
ele = symbol[0].upper()
#reset existing dictionnary
if 'rays' in dict:
for rays in dict['rays']:
for transition in dict[rays]:
#print "transition deleted = ",transition
del dict[transition]
#print "rays deleted = ",rays
del dict[rays]
#fill the dictionnary
dict['rays']=[]
z = getz(ele)
for n in range(len(ElementXrays)):
rays = ElementXrays[n]
if (rays == 'L xrays'):
shellrates = getElementLShellRates(ele,energy=energy,photoweights=photoweights)
elif (rays == 'M xrays'):
shellrates = getElementMShellRates(ele,energy=energy,photoweights=photoweights)
else:
shellrates = ElementShellRates[n][z-1]
shelltransitions = ElementShellTransitions[n]
dict[rays] = []
if 'TOTAL' in shelltransitions:
transitionoffset = 2
else:
transitionoffset = 1
maxrate = max(shellrates[transitionoffset:])
cum = 0.0
if maxrate > minrate:
for i in range(transitionoffset, len(shelltransitions)):
rate = shellrates [i]
if (rate/maxrate) > minrate:
transition = shelltransitions[i]
if (rays == "Ka xrays"):
xenergy = getxrayenergy(ele,transition.replace('a',''))
elif (rays == "Kb xrays"):
xenergy = getxrayenergy(ele,transition.replace('b',''))
else:
xenergy = getxrayenergy(ele,transition.replace('*',''))
if (xenergy > minenergy) or (n == 0) :
dict[transition] = {}
dict[rays].append(transition)
dict[transition]['energy'] = xenergy
dict[transition]['rate'] = rate
cum += rate
if rays not in dict['rays']:
dict['rays'].append(rays)
#cum = 1.00
if normalize:
if cum > 0.0:
for transition in dict[rays]:
dict[transition]['rate'] /= cum
dict['buildparameters']={}
dict['buildparameters']['energy'] = energy
dict['buildparameters']['minenergy'] = minenergy
dict['buildparameters']['minrate'] = minrate
def updateDict(energy=None, minenergy=MINENERGY, minrate=0.0010, cb=True):
for ele in ElementList:
_updateElementDict(ele, Element[ele], energy=energy, minenergy=minenergy, minrate=minrate)
if cb:
_updateCallback()
return
def _getMaterialDict():
cDict = ConfigDict.ConfigDict()
dirmod = PyMcaDataDir.PYMCA_DATA_DIR
matdict = os.path.join(dirmod,"attdata")
matdict = os.path.join(matdict,"MATERIALS.DICT")
if not os.path.exists(matdict):
#freeze does bad things with the path ...
dirmod = os.path.dirname(dirmod)
matdict = os.path.join(dirmod, "attdata")
matdict = os.path.join(matdict, "MATERIALS.DICT")
if not os.path.exists(matdict):
if dirmod.lower().endswith(".zip"):
dirmod = os.path.dirname(dirmod)
matdict = os.path.join(dirmod, "attdata")
matdict = os.path.join(matdict, "MATERIALS.DICT")
if not os.path.exists(matdict):
print("Cannot find file ", matdict)
#raise IOError("Cannot find %s" % matdict)
return {}
cDict.read(matdict)
return cDict
class BoundMethodWeakref:
"""Helper class to get a weakref to a bound method"""
def __init__(self, bound_method, onDelete=None):
def remove(ref):
if self.deleteCb is not None:
self.deleteCb(self)
self.deleteCb = onDelete
self.func_ref = weakref.ref(bound_method.im_func, remove)
self.obj_ref = weakref.ref(bound_method.im_self, remove)
def __call__(self):
obj = self.obj_ref()
if obj is not None:
func = self.func_ref()
if func is not None:
return func.__get__(obj)
def __cmp__( self, other ):
"""Compare with another reference"""
if not isinstance (other,self.__class__):
return cmp( self.__class__, type(other) )
return cmp( self.func_ref, other.func_ref) and cmp( self.obj_ref, other.obj_ref)
_registeredCallbacks=[]
def registerUpdate(callback):
if not hasattr(callback, "__call__"):
raise TypeError("It should be a callable method")
def delCallback(ref):
try:
i = _registeredCallbacks.index(ref)
del _registeredCallbacks[i]
except:
pass
if hasattr(callback, 'im_self') and callback.im_self is not None:
ref = BoundMethodWeakref(callback, delCallback)
else:
# function weakref
ref = weakref.ref(callback, delCallback)
if ref not in _registeredCallbacks:
_registeredCallbacks.append(ref)
def _updateCallback():
for methodref in _registeredCallbacks:
method = methodref()
if method is not None:
method()
Element={}
for ele in ElementList:
z = getz(ele)
Element[ele]={}
Element[ele]['Z'] = z
Element[ele]['name'] = ElementsInfo[z-1][4]
Element[ele]['mass'] = ElementsInfo[z-1][5]
Element[ele]['density'] = ElementsInfo[z-1][6]/1000.
Element[ele]['binding'] = {}
i=0
for shell in ElementShells:
i = i + 1
if z > len(ElementBinding):
#Give the bindings of the last element
Element[ele]['binding'][shell] = ElementBinding[-1][i]
else:
Element[ele]['binding'][shell] = ElementBinding[z-1][i]
#fluorescence yields
Element[ele]['omegak'] = getomegak(ele)
Element[ele]['omegal1'] = getomegal1(ele)
Element[ele]['omegal2'] = getomegal2(ele)
Element[ele]['omegal3'] = getomegal3(ele)
Element[ele]['omegam1'] = getomegam1(ele)
Element[ele]['omegam2'] = getomegam2(ele)
Element[ele]['omegam3'] = getomegam3(ele)
Element[ele]['omegam4'] = getomegam4(ele)
Element[ele]['omegam5'] = getomegam5(ele)
#Coster-Kronig
Element[ele]['CosterKronig'] = {}
Element[ele]['CosterKronig']['L'] = getCosterKronig(ele)
Element[ele]['CosterKronig']['M'] = MShell.getCosterKronig(ele)
#jump ratios
#xrays
#Element[ele]['rays']=[]
#updateElementDict(ele, Element[ele], energy=None, minenergy=0.399, minrate=0.001,cb=False)
Material = _getMaterialDict()
updateDict()
if __name__ == "__main__":
if len(sys.argv) > 1:
ele = sys.argv[1]
if ele in Element.keys():
print("Symbol = ",getsymbol(getz(ele)))
print("Atomic Number = ",getz(ele))
print("Name = ",getname(getz(ele)))
print("K-shell yield = ",Element[ele]['omegak'])
print("L1-shell yield = ",Element[ele]['omegal1'])
print("L2-shell yield = ",Element[ele]['omegal2'])
print("L3-shell yield = ",Element[ele]['omegal3'])
print("M1-shell yield = ",Element[ele]['omegam1'])
print("M2-shell yield = ",Element[ele]['omegam2'])
print("M3-shell yield = ",Element[ele]['omegam3'])
print("M4-shell yield = ",Element[ele]['omegam4'])
print("M5-shell yield = ",Element[ele]['omegam5'])
print("L Coster-Kronig= ",Element[ele]['CosterKronig']['L'])
print("M Coster-Kronig= ",Element[ele]['CosterKronig']['M'])
if len(sys.argv) > 2:
def testCallback():
print("callback called")
registerUpdate(testCallback)
e = float(sys.argv[2])
if 0:
_updateElementDict(ele,Element[ele],energy=e)
else:
import time
t0=time.time()
updateDict(energy=e)
print("update took ",time.time() - t0)
for rays in Element[ele]['rays']:
print(rays,":")
for transition in Element[ele][rays]:
print("%s energy = %.5f rate = %.5f" %\
(transition,Element[ele][transition]['energy'],
Element[ele][transition]['rate']))
if len(sys.argv) > 2:
LOGLOG = False
print("OLD VALUES")
print(getmassattcoef(ele,float(sys.argv[2])))
LOGLOG = True
print("NEW VALUES")
print(getmassattcoef(ele,float(sys.argv[2])))
if len(sys.argv) >3:
print(getcandidates(float(sys.argv[2]),
threshold=float(sys.argv[3])))
else:
print(getcandidates(float(sys.argv[2])))
else:
print(getmassattcoef(ele,[10.,11,12,12.5]))
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