def defineMat(elms, qty, name, density=None):
# Note: epq.Composition is designed to work with **mass fractions**
# Note: epq.Composition(Element[] elms, double[] massFracs)
c = epq.Composition(map(element, elms), qty, name)
if density:
c = epq.Material(c, epq.ToSI.gPerCC(density))
return (c)
def create_material_from_mf(l_comp, l_mf, density, name):
"""
create_material_from_mf(l_comp, l_mf, density, name)
Create a material from lists of compositions and mass fractions
and the density and a name.
Input
-----
l_comp A list of compositions.
l_mf A list of mass fractions.
density A number. The density in g/cm3
name A string. The name for the material. Use letters and numbers
without spaces or + or -. Simple mnemonics are better.
Return
------
A material
Example
-------
# Note: composition came from J. Donovan: Std 160 NBS K-412 mineral glass
l_comps = [epq.Element.O, epq.Element.Si, epq.Element.Mg, epq.Element.Ca,
epq.Element.Fe, epq.Element.Al, epq.Element.Mn, epq.Element.Na]
l_mfs = [0.43597 ,0.21199 ,0.11657 ,0.10899,
0.07742, 0.04906, 0.00077, 0.00043]
mat = create_material_from_mf(l_comps, l_mfs, 2.66, "K412")
print(mat)
print(mat.toHTMLTable())
"""
comp = epq.Composition(l_comp, l_mf)
mat = epq.Material(comp, epq.ToSI.gPerCC(density))
mat.setName(name)
return(mat)
defaultXtraParams = {}
if 'defaultBremFluor' not in globals():
defaultBremFluor = False
if 'defaultCharFluor' not in globals():
defaultCharFluor = False
if 'defaultNumTraj' not in globals():
defaultNumTraj = 1000
if 'defaultDose' not in globals():
defaultDose = 120.0
# start clean
DataManager.clearSpectrumList()
pet = epq.Material(epq.Composition([epq.Element.C,epq.Element.H,epq.Element.O],[0.62502,0.04196,0.069042]),epq.ToSI.gPerCC(1.37))
cu = epq.Material(epq.Composition([epq.Element.Cu],[1.0],"Cu"), epq.ToSI.gPerCC(8.96))
pd = epq.Material(epq.Composition([epq.Element.Pd],[1.0],"Pd"), epq.ToSI.gPerCC(11.9))
ag = epq.Material(epq.Composition([epq.Element.Ag],[1.0],"Ag"), epq.ToSI.gPerCC(10.5))
# define the desired transitions
xrts=mc3.suggestTransitions("COCuPdAg")
# print(xrts)
# set up the extra parameters
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
nTraj = 250 # num Traj to run per pt 10000 for a long run
charF = True # include characteristic fluorescence
bremF = True # include continuum fluorescence
pc = 2.5 # nA
lt = 100.0 # sec
e0 = 7.0 # keV
imgSize = 512 # pixel size for images
imgSzUm = 5.0 # image size in microns
vmrlEl = 40 # number of el for VMRL
dose = pc * lt # nA sec
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/"
simDir = gitDir + relPrj + "/"
jmg.ensureDir(simDir)
wd = gitDir + relPrj
os.chdir(wd)
pyrDir = wd + "/sim-multifilm-on-sub Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
# start clean
DataManager.clearSpectrumList()
al2o3 = epq.Material(
epq.Composition([epq.Element.Al, epq.Element.O], [0.5293, 0.4707]),
epq.ToSI.gPerCC(3.95))
al = epq.Material(epq.Composition([epq.Element.Al], [1.0], "Al"),
epq.ToSI.gPerCC(2.7))
jmg.ensureDir(datDir)
jmg.ensureDir(csvDir)
jmg.ensureDir(simDir)
jmg.ensureDir(msaDir)
wd = gitDir + relPrj
os.chdir(wd)
pyrDir = wd + "/simCoatedOverBlock Results"
det = findDetector("Oxford p4 05eV 2K")
# det = findDetector("Si(Li)") # test with default
print(det)
pet = epq.Material(
epq.Composition([epq.Element.C, epq.Element.H, epq.Element.O],
[0.62502, 0.04196, 0.069042]), epq.ToSI.gPerCC(1.37))
pet.setName("PET")
al2o3 = epq.Material(
epq.Composition([epq.Element.Al, epq.Element.O], [0.5293, 0.4707]),
epq.ToSI.gPerCC(3.95))
al2o3.setName("Al2O3")
ag = epq.Material(epq.Composition([epq.Element.Ag], [1.0], "Ag"),
epq.ToSI.gPerCC(11.9))
ag.setName("Ag")
# start clean
DataManager.clearSpectrumList()
# define the desired transitions (most intense for each line...)
# Ka1 Ka1 Ka1 La1
xrts = [
transition("C K-L3"),
if 'defaultXtraParams' not in globals():
defaultXtraParams = {}
if 'defaultBremFluor' not in globals():
defaultBremFluor = False
if 'defaultCharFluor' not in globals():
defaultCharFluor = False
if 'defaultNumTraj' not in globals():
defaultNumTraj = 1000
if 'defaultDose' not in globals():
defaultDose = 120.0
# start clean
DataManager.clearSpectrumList()
pet = epq.Material(
epq.Composition([epq.Element.C, epq.Element.H, epq.Element.O],
[0.62502, 0.04196, 0.069042]), epq.ToSI.gPerCC(1.37))
cu = epq.Material(epq.Composition([epq.Element.Cu], [1.0], "Cu"),
epq.ToSI.gPerCC(8.96))
ag = epq.Material(epq.Composition([epq.Element.Ag], [1.0], "Ag"),
epq.ToSI.gPerCC(11.9))
# define the desired transitions
xrts = mc3.suggestTransitions("COCuAg")
# print(xrts)
# set up the extra parameters
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=charF,
charFluorAccum=charF,
bremFluorAccum=bremF))
import gov.nist.microanalysis.EPQLibrary as epq
# Density from Probe Software, compo from NIST spectrum
k412 = epq.Material(epq.Composition([epq.Element.O,
epq.Element.Mg,
epq.Element.Al,
epq.Element.Si,
epq.Element.Ca,
epq.Element.Fe],
[ 0.4276,
0.1166,
0.0491,
0.2120,
0.1090,
0.0774]
),
epq.ToSI.gPerCC(2.600))
k412.setName("K412")
def defineMat(elms, qty, name, density=None):
c = epq.Composition(map(element, elms), qty, name)
if density:
c = epq.Material(c, epq.ToSI.gPerCC(density))
return (c)
DataManager.clearSpectrumList()
eagleXG = epq.Material(epq.Composition([epq.Element.O,
epq.Element.Si,
epq.Element.Al,
epq.Element.Ca,
epq.Element.B,
epq.Element.Mg,
epq.Element.Sr,
epq.Element.Sn,
epq.Element.Ba,
epq.Element.As,
epq.Element.Sb,
epq.Element.Fe,
epq.Element.Zr,
epq.Element.Ti],
[0.518777,
0.301391,
0.090081,
0.038763,
0.032655,
0.007728,
0.006965,
0.001198,
0.001092,
0.000238,
0.000387,
0.000355,
0.000218,
0.000152]),
epq.ToSI.gPerCC(2.38))
eagleXG.setName("EagleXG")
XRAY: ka ka ka ka ka ka ka
ELWT: 36.020 2.230 11.550 18.400 1.510 10.510 19.790
KFAC: .1934 .0132 .0797 .1364 .0145 .0915 .1743
ZCOR: 1.8621 1.6868 1.4499 1.3489 1.0384 1.1485 1.1353
AT% : 56.147 2.288 10.676 16.339 .940 4.771 8.838
"""
garnet = epq.Material(epq.Composition([epq.Element.O,
epq.Element.Mg,
epq.Element.Al,
epq.Element.Si,
epq.Element.Ca,
epq.Element.Mn,
epq.Element.Fe],
[ 0.3602,
0.0223,
0.1155,
0.1840,
0.0151,
0.1051,
0.1979]), epq.ToSI.gPerCC(3.56))
garnet.setName("garnet")
trs = majorTransitions(garnet, e0, trs=(epq.XRayTransition.KA1, epq.XRayTransition.KB1, epq.XRayTransition.LA1, epq.XRayTransition.MA1), thresh=1.0)
garnetSpc = mc3.simulate(garnet, det, e0=e0, dose=dose, withPoisson=True, nTraj=nTraj, sf=charF, bf=bremF, xtraParams={})
sp=garnetSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName,"garent-std")
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
lt = 100 # sec
pc = 1.0 # nA
tNmC = 20 # nm C
przDepUm = 2.0 # depth for phi-rho-z images in microns
imgSzUm = 2.0 # size for emission images in microns
imgSize = 512 # pixel size for images
vmrlEl = 40 # number of el for VMRL
resln = 1.0 # factor for phirhoz resln
dose = pc * lt # na-sec"
DataManager.clearSpectrumList()
apatite = epq.Material(
epq.Composition([
epq.Element.O, epq.Element.Ca, epq.Element.P, epq.Element.F,
epq.Element.Sr
], [0.39368, 0.38936, 0.17863, 0.03700, 0.00133]), epq.ToSI.gPerCC(3.15))
apatite.setName("apatite")
k411 = epq.Material(
epq.Composition([
epq.Element.O, epq.Element.Si, epq.Element.Fe, epq.Element.Ca,
epq.Element.Mg
], [0.435581, 0.25382, 0.11209, 0.11057, 0.08847]), epq.ToSI.gPerCC(2.6))
k411.setName("K411")
mgo = material("MgO", density=3.58)
c = material("C", density=2.1)
si = material("Si", density=2.329)
fe = material("Fe", density=7.86)
caf2 = material("CaF2", density=3.18)
pyrDir = datDir + "/makeFastTestCube Results"
e0 = 20.0
pc = 1.0
lt = 30.0
det = findDetector("Oxford p4 05eV 2K")
cw = det.getChannelWidth()
dp = det.getProperties()
resn = dp.getNumericProperty(epq.SpectrumProperties.Resolution)
rplFil = datDir + "/CuAl.rpl"
rawFil = datDir + "/CuAl.raw"
DataManager.clearSpectrumList()
# make the materials
cu = epq.Material(epq.Composition([epq.Element.Cu], [1.0]),
epq.ToSI.gPerCC(8.096))
cuSpc = simulate(cu, det, keV=e0, dose=lt * pc, withPoisson=True)
cuSpc.rename("ana sim Cu")
al = epq.Material(epq.Composition([epq.Element.Al], [1.0]),
epq.ToSI.gPerCC(2.70))
alSpc = simulate(al, det, keV=e0, dose=lt * pc, withPoisson=True)
alSpc.rename("ana sim Al")
# display(cuSpc)
# display(alSpc)
res = et.RippleFile(64, 64, 2048, et.RippleFile.UNSIGNED, 4,
et.RippleFile.BIG_ENDIAN, rplFil, rawFil)
for x in range(-32, 32, 1):
print "Working on row %d" % (x)
relPrj = "/dtsa2Scripts/utility"
prjDir = gitDir + relPrj
rptDir = prjDir + '/testAlgorithms Results/'
e0 = 15 # kV
# Define the material k412
# Density from Probe Software, compo from NIST spectrum
k412 = epq.Material(epq.Composition([epq.Element.O,
epq.Element.Mg,
epq.Element.Al,
epq.Element.Ca,
epq.Element.Si,
epq.Element.Fe],
[ 0.427580,
0.116567,
0.049062,
0.211982,
0.108990,
0.077420]
),
epq.ToSI.gPerCC(2.600))
k412.setName("K412")
au = epq.Material(epq.Composition([epq.Element.Au], [1.0]), epq.ToSI.gPerCC(19.30))
au.setName("Au")
def ComputeElectronRange(mat, e0):
"""ComputeElectronRange(mat, e0)
Compute the electron range for a material using two
simDir = gitDir + relPrj + "/"
ensureDir(simDir)
ensureDir(datDir)
wd = gitDir + relPrj + "/py"
os.chdir(wd)
pyrDir = wd + "/sim-C-on-Cu-w-Img Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
# start clean
DataManager.clearSpectrumList()
# create the materials
c = epq.Material(epq.Composition([epq.Element.C], [1.0], "C"),
epq.ToSI.gPerCC(2.25))
cu = epq.Material(epq.Composition([epq.Element.Cu], [1.0], "Cu"),
epq.ToSI.gPerCC(8.96))
# define the desired transitions
xrts = mc3.suggestTransitions("CCu")
# set up the extra parameters
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=charF,
charFluorAccum=charF,
bremFluorAccum=bremF))
# note that the image size on the specimen is in meters...
for name in glob.glob(spcDir + '/*.msa'):
name = name.replace('\\', '/')
bn = os.path.basename(name)
x = bn.split('-')
sDate = "%s-%s-%s" % (x[0], x[1], x[2])
lDate.append(sDate)
spc = wrap(readSpectrum(name))
sp = spc.getProperties()
pc = sp.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
lt = sp.getNumericProperty(epq.SpectrumProperties.LiveTime)
sp.setDetector(det)
spc.rename(sDate)
if bDisplayAll:
display(spc)
comp = epq.Composition(epq.Element.Cu)
sf = epq.SpectrumFitter8(det, comp, spc)
rois = sf.getROIS()
props = sp.getDetector().getCalibration().getProperties()
offset = props.getNumericWithDefault(epq.SpectrumProperties.EnergyOffset,
0.0)
gain = props.getNumericWithDefault(epq.SpectrumProperties.EnergyScale,
10.0)
coeffs = [offset, gain]
sf.setEnergyScale(epq.SpectrumFitter8.EnergyScaleFunction(coeffs, 2))
sf.setResolution(epq.SpectrumFitter8.FanoNoiseWidth(6.0))
sf.setMultiLineset(sf.buildWeighted(rois))
results = sf.compute()
# sf.setEnergyScale(epq.SpectrumFitter8.AltEnergyScaleFunction(coeffs))
# print(dir(results))
# ['FWHMatMnKa', '__class__', '__copy__', '__deepcopy__', '__delattr__',
det,
e0=e0,
dose=dose,
withPoisson=True,
nTraj=nTraj,
sf=charF,
bf=bremF,
xtraParams={})
sp = siSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, "Si-std")
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
sp.setNumericProperty(epq.SpectrumProperties.FaradayEnd, dose)
sp.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
sp.setCompositionProperty(epq.SpectrumProperties.StandardComposition,
epq.Composition(epq.Element.Si))
display(siSpc)
siStd = {"El": element("Si"), "Spc": siSpc}
sic = epq.Material(
epq.Composition([epq.Element.Si, epq.Element.C], [0.70045, 0.29955]),
epq.ToSI.gPerCC(3.21))
sic.setName("SiC")
sicSpc = mc3.simulate(sic, det, e0, dose, True, nTraj, True, True, {})
sp = sicSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, "SiC-std")
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
sp.setNumericProperty(epq.SpectrumProperties.FaradayEnd, dose)
sp.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
nTraj = 10000 # trajectories
lt = 60 # sec
pc = 0.25 # nA
tNmTa = 2
tNmC = 10
tNmAuPd = 10
tNmSiO2 = 100
dose = pc * lt # na-sec"
DataManager.clearSpectrumList()
sio2 = material("SiO2", density=2.65)
c = material("C", density=2.1)
aupd = epq.Material(
epq.Composition([epq.Element.Au, epq.Element.Pd], [0.60, 0.40]),
epq.ToSI.gPerCC(0.6 * 19.30 + 0.4 * 11.9))
ta = material("Ta", density=16.4)
layers = [[sio2, tNmSiO2 * 1.0e-9], [c, 50.0e-6]]
# multiFilm(layers, det, e0=20.0, withPoisson=True,
# nTraj=defaultNumTraj, dose=defaultDose,
# sf=defaultCharFluor, bf=defaultBremFluor,
# xtraParams=defaultXtraParams)
basSim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
det,
e0=e0,
dose=dose,
withPoisson=True,
nTraj=nTraj,
sf=charF,
bf=bremF,
xtraParams={})
sp = auSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, "Au-std")
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
sp.setNumericProperty(epq.SpectrumProperties.FaradayEnd, dose)
sp.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
sp.setCompositionProperty(epq.SpectrumProperties.StandardComposition,
epq.Composition(epq.Element.Au))
display(auSpc)
auStd = {"El": element("Au"), "Spc": auSpc}
cuSpc = mc3.simulate(cu,
det,
e0=e0,
dose=dose,
withPoisson=True,
nTraj=nTraj,
sf=charF,
bf=bremF,
xtraParams={})
sp = cuSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, "Cu-std")
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
pc = 1.5 # nA
lt = 100. # sec
dose = lt*pc # nA*sec
imgSize = 512 # pixel size for images
imgSzUm = 0.25
charF = True # include characteristic fluorescence
bremF = True # include continuum fluorescence
poisN = True # include Poisson noise
vmrlEl = 100 # number of el for VMRL
sc = 1.0e-06 # um to meters
umLine = nmLinWid * 1.0e-03
linMat = "Pd"
blkMat = "Cu"
lin = epq.Material(epq.Composition([epq.Element.Pd],[1.0],"Pd"), epq.ToSI.gPerCC(12.023))
blk = epq.Material(epq.Composition([epq.Element.Cu],[1.0],"Cu"), epq.ToSI.gPerCC(8.96))
det = findDetector("Oxford p4 05eV 2K")
print(det)
homDir = os.environ['HOME']
relPrj = "/work/proj/QM15-04-07A-Ciminelli"
simDir = homDir + relPrj + "/dat/simDir"
csvDir = homDir + relPrj + "/dat/csv"
jmg.ensureDir(simDir)
jmg.ensureDir(csvDir)
# wd = homDir + relPrj + "/py/dtsa"
wd = homDir + relPrj + "/py/dtsa"
os.chdir(wd)
# strCmpd = "C395O130F660"
#
# PTFE
# elements = [epq.Element.C, epq.Element.F]
# strName = "PTFE"
# strCmpd = "C2F4"
# elements = [epq.Element.Cu, epq.Element.O]
# strName = "Cu(OH)2"
# strCmpd = "Cu(OH)2"
# massFra = jmg.getMassFractions(strCmpd, elements, 5)
kapton = epq.Material(
epq.Composition(
[epq.Element.C, epq.Element.O, epq.Element.N, epq.Element.H],
[0.69113, 0.20924, 0.07327, 0.02636]), epq.ToSI.gPerCC(1.420))
kapton.setName("Kapton")
# from Wikepedia from Corning and Schott
pyrex = epq.Material(
epq.Composition([
epq.Element.B, epq.Element.O, epq.Element.Na, epq.Element.Mg,
epq.Element.Al, epq.Element.Si, epq.Element.Cl, epq.Element.Ca,
epq.Element.Fe
], [
0.03920, 0.53850, 0.03120, 0.00030, 0.01170, 0.37720, 0.00100, 0.00070,
0.00030
]), epq.ToSI.gPerCC(2.30))
pyrex.setName("Pyrex")
