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 minEdge(elm):
"""Example: minEdge("Ag")
Returns the lowest energy edge which is likely to be visible in an
EDS detector for the specified element"""
elm = dtsa2.element(elm)
if elm.getAtomicNumber() >= MinMElement:
res = epq.AtomicShell(elm, epq.AtomicShell.MV)
elif elm.getAtomicNumber() >= MinLElement:
res = epq.AtomicShell(elm, epq.AtomicShell.LIII)
else:
res = epq.AtomicShell(elm, epq.AtomicShell.K)
return res
def WDSCrystal(xrt, n=1, R=RolandCircleRadius):
"""Synatx: WDSCrystal(xrt,n=1,[R=RolandCircleRadius])
Prints a list of the WDS crystals alternatives along with
the associated L-value. (Note: xrt may be an element or
an XRayTransitionSet (see getTransitionSet(...))"""
xrts = []
if isinstance(xrt, epq.XRayTransition):
xrts = xrts + [xrt]
elif isinstance(xrt, str) or isinstance(xrt, epq.Element):
elm = dtsa2.element(xrt)
for tr in [epq.XRayTransition.KA1, epq.XRayTransition.LA1, epq.XRayTransition.MA1]:
if epq.XRayTransition.exists(elm, tr):
xrts = xrts + [epq.XRayTransition(elm, tr)]
elif isinstance(xrt, epq.XRayTransitionSet):
xrts = xrt.getTransitions()
else:
print "Invalid argument: %s" % xrt
return
zippo = True
for cry, twoD in TwoDSpacing.iteritems():
for tr in xrts:
L = WDS_L(cry, tr, n, R)
if (L > 60) and (L < 260):
if zippo:
print "Crystal\tLine\tL Value"
zippo = False
print "%s\t%s\t%3.6g" % (cry, tr, L)
if zippo:
print "None"
def maxEdge(elm, e0, over=1.5):
"""Example: maxEdge("Ag", 20.0, 1.5)
Returns the highest energy edge which is excited with the overvoltage
specified (1.5) for the specified beam energy (20.0)."""
elm = dtsa2.element(elm)
e0 = epq.ToSI.keV(e0)
res = None
if elm.getAtomicNumber() > MinMElement:
sh = epq.AtomicShell.MV
if epq.AtomicShell.getEdgeEnergy(elm, sh) * over <= e0:
res = epq.AtomicShell(elm, sh)
if elm.getAtomicNumber() > MinLElement:
sh = epq.AtomicShell.LIII
if epq.AtomicShell.getEdgeEnergy(elm, sh) * over <= e0:
res = epq.AtomicShell(elm, sh)
sh = epq.AtomicShell.K
if epq.AtomicShell.getEdgeEnergy(elm, sh) * over <= e0:
res = epq.AtomicShell(elm, sh)
return res
def openRipple(rpl, e0, i0, liveTime, det):
"""openRipple(rpl, e0, i0, liveTime, det)
Open a ripple file as an ISpectrumData object with setPosition(x,y) to permit navigating /
through the spectra."""
sp = epq.SpectrumProperties()
sp.setDetector(det)
sp.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, i0)
sp.setNumericProperty(epq.SpectrumProperties.LiveTime, liveTime)
return ept.RippleSpectrum(rpl, sp)
def maxPixel(rpl):
"""maxPixel(rpl)
Computes the max pixel spectrum for the specified ripple/raw spectrum object."""
xs = epq.ExtremumSpectrum()
for r in xrange(0, rpl.getRows()):
dt2.StdOut.append(".")
if dt2.terminated:
break
for c in xrange(0, rpl.getColumns()):
rpl.setPosition(r, c)
xs.include(rpl)
return xs
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)
def suggestTransitionSets(mat, e0=20.0):
"""suggestTransitions(mat, e0=20.0)
Suggest a list of XRayTransitionSet objects for the specified material."""
mat = dtsa2.material(mat)
fams = ("Ka", "Kb", "La", "Lb", "Ma", "Mb")
res = []
for elm in mat.getElementSet():
for fam in fams:
xrts = dtsa2.getTransitionSet(elm, fam)
removeMe = epq.XRayTransitionSet()
if (xrts.size() > 0):
for xrt in xrts:
ee = epq.FromSI.keV(xrt.getEnergy())
if (ee < 0.2) or (ee > 0.95 * e0):
removeMe.add(xrt)
if removeMe.size() > 0:
xrts.removeAll(removeMe)
if xrts.size() > 0:
res.append(xrts)
return res
def rippleToMaps(rpl, vecSet, step=1):
"""RippleToMaps(rpl, vecSet, step=1)
Applies a vector set to a RPL/RAW file pair producing a dictionary of MapImage objects /
indexed by RegionOfInterest objects."""
width = rpl.getColumns()
height = rpl.getRows()
vecs = vecSet.getVectors()
planes = epq.MapImage(width, height, len(vecs), str(vecSet))
rpl.setSpan(step, step)
for r in xrange(0, height, step):
if dt2.isTerminated():
break
for c in xrange(0, width, step):
if dt2.isTerminated():
break
rpl.setPosition(r, c)
krs = vecSet.getKRatios(rpl)
kra = []
for vec in vecs:
kra.append(krs.getKRatio(vec.getROI()))
planes.inc(c, r, kra)
return planes
def createGas(comp, pascal):
"""createGas(comp, pascal)
Create a gas from a composition at the specified pressure in Pascal at 300 K.
Ex: createGas("H2O", 0.1)"""
return epq.Gas(dtsa2.material(comp), pascal, 300.0)
lT = [] # will have t=0...
lPICmu = [] # an array for mean C peak integral
lPICuc = [] # an array for C peak integral uncertainty
lPISimu = [] # an array for mean Cu peak integral
lPISiuc = [] # an array for Cu peak integral uncertainty
# empty xtra-param
xp = {}
# empty x-ray transition set
xrts = []
# set a counter
iCount = 0
# get and add the C-K family
cTS = epq.XRayTransitionSet(epq.Element.C, epq.XRayTransitionSet.K_FAMILY)
cTrs = cTS.getTransitions()
for tr in cTrs:
xrts.append(tr)
# get and add the Cu-L family
siTS = epq.XRayTransitionSet(epq.Element.Si, epq.XRayTransitionSet.K_FAMILY)
siTrs = siTS.getTransitions()
for tr in siTrs:
xrts.append(tr)
xp.update(
mc3.configureXRayAccumulators(xrts,
charAccum=True,
charFluorAccum=True,
bremFluorAccum=True))
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,
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))
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)
os.chdir(wrkDir)
przDir = wrkDir + '/prz/'
# Save spectra in sim directory
jmg.ensureDir(przDir)
# jmg.ensureDir(rptDir)
det = findDetector("Oxford p4 05eV 4K")
e0 = 7 # kV
nSteps = e0*100 # steps
rho = 2.6 # sec
l_comps = [epq.Element.Al, epq.Element.Mg, epq.Element.P, epq.Element.O]
l_mfs = [ 0.06470, 0.06650, 0.32900, 0.5390]
k496 = jmg.create_material_from_mf(l_comps, l_mfs, 2.6, "K-496")
xrts = mc3.suggestTransitions(k496)
a = jmg.compPhiRhoZ(k496, det, e0, nSteps, xrts, alg=epq.PAP1991(), base="pap-prz", outdir=przDir)
# clean up cruft
# shutil.rmtree(rptDir)
print "Done!"
end = time.time()
delta = (end-start)/60
msg = "This script required %.3f min" % delta
print msg
if(delta > 60):
delta = delta/60
msg = "...or %.3f hr" % delta
print msg
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)
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)
for y in range(-32, 32, 1):
sim.getProperties().setTextProperty(epq.SpectrumProperties.SpectrumComment,
amcThickComment)
return sim
start = time.time()
DataManager.clearSpectrumList()
c = material("C", density=2.266)
fe = material("Fe", density=7.86)
fe3c = material("Fe3C", density=4.93)
# only get FeL at 7 kV
trs = [
epq.XRayTransitionSet(epq.Element.C, epq.XRayTransitionSet.K_FAMILY),
epq.XRayTransitionSet(epq.Element.Fe, epq.XRayTransitionSet.L_FAMILY)
]
# First simulate the standards
# Start with C
startCycle = time.time()
c_std_spc = jm3.simBulkStd(c, det, e0, nTraj, lt=lt, pc=pc)
display(c_std_spc)
sName = "%s-std-%g-kV-%g-traj" % ("C", e0, nTraj)
fi = basePath + "/"
fi += sName
fi += ".msa"
if bSaveSpc == True:
c_std_spc.save(fi)
endCycle = time.time()
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 = [
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))
charF = True # include characteristic fluorescence
bremF = True # include continuum fluorescence cd ..
pc = 2.5 # nA
lt = 100.0 # sec
e0 = 3.0 # keV
dose = pc * lt # nA sec
# start clean
DataManager.clearSpectrumList()
# create the materials
si = material("Si", density=2.32)
sic = material("SiC", density=3.21)
trs = [
epq.XRayTransitionSet(epq.Element.C, epq.XRayTransitionSet.K_ALPHA),
epq.XRayTransitionSet(epq.Element.O, epq.XRayTransitionSet.K_ALPHA),
epq.XRayTransitionSet(epq.Element.Si, epq.XRayTransitionSet.K_ALPHA)
]
# start with bulk standards
#
# C
siSpc = mc3.simulate(si,
det,
e0=e0,
dose=dose,
withPoisson=True,
nTraj=nTraj,
sf=charF,
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__',
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)
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...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
def createMonatomicGas(elm, pascal):
"""createMonatomicGas(elm, pascal)
Create a gas of single atoms of the specified element at the specified pressure in Pascal and 300 K"""
return epq.Gas((elm,), (1,), pascal, 300.0, elm.toString() + " gas at %f Pa" % pascal)
nTraj = 100 # 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 = 15.0 # keV
dose = pc * lt # nA sec
# start clean
DataManager.clearSpectrumList()
# create the materials
ag = material("Ag", density=10.5)
trs = [
epq.XRayTransitionSet(epq.Element.Au, epq.XRayTransitionSet.L_ALPHA),
epq.XRayTransitionSet(epq.Element.Cu, epq.XRayTransitionSet.K_ALPHA)
]
# start with bulk standards
#
# Au
auSpc = mc3.simulate(au,
det,
e0=e0,
dose=dose,
withPoisson=True,
nTraj=nTraj,
sf=charF,
bf=bremF,
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
algorithms.
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)
nm3.EmissionImageBase.useHeatMapPalette()
def configureVoxelated(dim=20, size=2.e-6, generated=True):
return { 'Voxelated' : dim, 'GeneratedV' : generated, 'SizeV' : size }
def configureVRML(nElectrons=40):
return { 'VRML' : nElectrons }
def toPascal(torr):
return torr * 133.32237
def toTorr(pascal):
return pascal / 133.32237
if 'defaultGas' not in globals():
defaultGas = epq.Gas((epq.Element.H, epq.Element.O,), (2, 1,), toPascal(0.1), 300.0, "Water vapor")
def createMonatomicGas(elm, pascal):
"""createMonatomicGas(elm, pascal)
Create a gas of single atoms of the specified element at the specified pressure in Pascal and 300 K"""
return epq.Gas((elm,), (1,), pascal, 300.0, elm.toString() + " gas at %f Pa" % pascal)
def createGas(comp, pascal):
"""createGas(comp, pascal)
Create a gas from a composition at the specified pressure in Pascal at 300 K.
Ex: createGas("H2O", 0.1)"""
return epq.Gas(dtsa2.material(comp), pascal, 300.0)
def configureVariablePressure(pathLength, gas=defaultGas):
return { 'VP' : (pathLength, gas) }
