def simSpc(mat, e0, det, dose, ntraj, simDir):
"""
simSpc(mat, e0, det, dose, ntraj, simDir)
simulate a spectrum from a material and write it out.
"""
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(mat, det, e0, dose, True, nTraj, True, True, xtraParams)
fmtS = "%s-at-%g-kV"
sName = fmtS % (mat.getName(), e0)
spc.rename(sName)
spc.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return spc
def simSpc(mat, e0, det, dose, ntraj, simDir):
"""
simSpc(mat, e0, det, dose, ntraj, simDir)
simulate a spectrum from a material and write it out.
"""
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(mat, det, e0, dose, True,
nTraj, True, True, xtraParams)
fmtS = "%s-at-%g-kV"
sName = fmtS % (mat.getName(), e0)
spc.rename(sName)
spc.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return spc
# wd = homDir + relPrj + "/py/dtsa"
wd = homDir + relPrj + "/py/dtsa"
os.chdir(wd)
pyrDir = wd + "/simPdLineInCuMatrix Results"
#start clean
DataManager.clearSpectrumList()
# xrts=mc3.suggestTransitions("PdCu")
xrts = [epq.XRayTransition(epq.Element.Cu, epq.XRayTransition.LA1), epq.XRayTransition(epq.Element.Pd, epq.XRayTransition.LA1)]
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=charF, charFluorAccum=charF, bremFluorAccum=bremF))
xtraParams.update(mc3.configureOutput(simDir))
xtraParams.update(mc3.configureBeam(0.5*nmLinWid*1.0e-9, 0, -0.099, 1.0))
# xtraParams.update(mc3.configureGun(gun))
# mc3.useHeatMapPalette()
print(xtraParams)
# spc = jm3.lineInMatrix(lin, blk, nmLinWid, umBlock, det, e0, withPoisson=True, nTraj=nTraj, dose=dose, sf=charF, bf=bremF, xtraParams=xtraParams)
# spc = jm3.lineInMatrix(lin, blk, nmLinWid, umBlock, det, e0, poisN, nTraj, dose, charF, bremF, xtraParams)
#e0=20.0, dose=defaultDose, withPoisson=poisN, nTraj=defaultNumTraj, sf=defaultCharFluor, bf=defaultBremFluor, xtraParams=defaultXtraParams):
# spc = mc3.simulate(blk, det, e0, dose, poisN, nTraj, charF, bremF, xtraParams)
#
# Embedded Rectangle
#
# This works as expected.
# spc = mc3.embeddedRectangle(lin, [umLine*sc, umBlock*sc, umBlock*sc], blk, 0, det, e0, withPoisson=poisN, nTraj=nTraj, dose=dose, sf=charF, bf=bremF, xtraParams=xtraParams)
rhoAu = 19.3
rhoCu = 8.95
SRM482A = material("Au",rhoAu)
SRM482B = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.801,0.198],"Au80Cu20"),epq.ToSI.gPerCC(0.8*rhoAu+0.2*rhoCu))
SRM482C = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.603,0.396],"Au60Cu40"),epq.ToSI.gPerCC(0.6*rhoAu+0.4*rhoCu))
SRM482D = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.401,0.599],"Au40Cu60"),epq.ToSI.gPerCC(0.4*rhoAu+0.6*rhoCu))
SRM482E = epq.Material(epq.Composition(map(element,["Au","Cu"],),[0.201,0.798],"Au20Cu80"),epq.ToSI.gPerCC(0.2*rhoAu+0.8*rhoCu))
SRM482F = material("Cu",rhoCu)
SRM482 = ( SRM482A, SRM482B, SRM482C, SRM482D, SRM482E, SRM482F, )
range = electronRange(SRM482A,e0,density=None)
xtraP = {}
xtraP.update(mc3.configureOutput(DefaultOutput))
xtraP.update(mc3.configurePhiRhoZ(1.5*range))
xtraP.update(mc3.configureEmissionImages(mc3.suggestTransitions(SRM482C,e0), 1.5*range, size = 512))
xtraP.update(mc3.configureTrajectoryImage(1.5*range, size = 512))
specs = {}
for mat in SRM482:
if terminated:
break
specs[mat] = mc3.simulate(mat, det,e0=e0, nTraj=nE, dose=500.0, sf=True, bf=True,xtraParams=xtraP)
specs[mat].save("%s/%s.msa" % ( DefaultOutput, specs[mat] ))
specs[mat].display()
unks = ( specs[SRM482B], specs[SRM482C], specs[SRM482D], specs[SRM482E] )
stds = { "Au" : specs[SRM482A], "Cu" : specs[SRM482F] }
def uncoatedSimBulkStd(mat,
det,
e0,
nTraj,
outPath,
dim=5.0e-6,
lt=100,
pc=1.0,
emiSize=512):
"""
uncoatedSimBulkStd(mat, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should
have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images in um
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.jmMC3 as jm3
outPath = "path/to/yours/spc"
cu = material("Cu", density=8.92)
det = findDetector("Si(Li)")
a = jm3.uncoatedSimBulkStd(cu, det, 15.0, 100, outPath,
dim=5.0e-6, lt=100,
pc=1.0, emiSize=512)
a.display()
"""
start = time.time()
strMat = mat.getName()
dose = pc * lt # na-sec"
# specify the transitions to generate
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
# At 20 kV the images are best at 2.0e-6
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, dim, emiSize))
xtraParams.update(mc3.configurePhiRhoZ(dim))
xtraParams.update(mc3.configureTrajectoryImage(dim, emiSize))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
print("Output sent to %s") % (outPath)
sim = mc3.simulate(mat, det, e0, lt * pc, True, nTraj, True, True,
xtraParams)
sName = "%s-%g-kV" % (strMat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
end = time.time()
delta = end - start
msg = "This simulation required %.f sec" % (delta)
print(msg)
msg = " %.f min" % (delta / 60.0)
print(msg)
msg = " %.f hr" % (delta / 360.0)
print("")
return (sim)
def simLineInMatrixLimScan(lin,
linMat,
blk,
blkMat,
nmLinWid,
umBlock,
nmScan,
nPts,
trs,
outDir,
hdr,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=100,
sf=True,
bf=True,
iDigits=5,
bVerbose=False,
xtraParams={}):
"""simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,
nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True,
nTraj=nTraj, sf=True, bf=True, iDigits=5, bVerbose=False,
xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'. We step a total
distance of nmScan across the center of the line.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra the scanned
region. It will then compute the K-ratios for each spectrum and write
them to a file `name' in outDir with a header `hdr' that matches the
transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
dose = lt * pc
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [
] # an array for the K-ratio of the block. Title correspond to hdr string
umLine = nmLinWid * 1.0e-3
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin,
linMat,
det,
e0,
lt,
pc,
withPoisson=withPoisson,
nTraj=nTraj,
sf=sf,
bf=bf,
xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk,
blkMat,
det,
e0,
lt,
pc,
withPoisson=withPoisson,
nTraj=nTraj,
sf=sf,
bf=sf,
xtraParams={})
dt2.display(blkStd)
lStd = {"El": dt2.element(linMat), "Spc": linStd}
bStd = {"El": dt2.element(blkMat), "Spc": blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts / 2, (nPts / 2) + 1, 1):
xPosNm = x * nmScan / nPts
lX.append(round(xPosNm, iDigits))
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(trs,
charAccum=sf,
charFluorAccum=sf,
bremFluorAccum=bf))
xtraParams.update(mc3.configureOutput(outDir))
xtraParams.update(mc3.configureBeam(xPosNm * 1.0e-09, 0, -0.099, 1.0))
spec = mc3.embeddedRectangle(lin,
[umLine * sc, umBlock * sc, umBlock * sc],
blk,
0,
det,
e0,
withPoisson=withPoisson,
nTraj=nTraj,
dose=dose,
sf=sf,
bf=bf,
xtraParams=xtraParams)
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount, xPosNm)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile = "%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (
nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f = open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.3f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
def fullSimBulkStd(mat, det, e0, nTraj, outPath, dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False):
"""
fullSimBulkStd(mat, det, e0, nTraj, outPath, dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should have a useful name.
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
ctd - Boolean (False) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.mcSimulate3 as mc3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = fullSimBulkStd(cu, det, 20.0, 100, 100, 1.0)
a.display()
"""
dose = pc * lt # na-sec"
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
mc3.configureEmissionImages(xrts, dim, emiSize)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, 5.0e-6, 512))
xtraParams.update(mc3.configurePhiRhoZ(5.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(5.0e-6, 512))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
mc3.configureOutput(outPath)
print("Output sent to %s") % (outPath)
dose = lt*pc
sim = mc3.simulate(mat, det, e0, dose, withPoisson=True, nTraj=nTraj,
sf=True, bf=True, xtraParams=xtraParams)
sName = "%s-%g-kV" % (mat, e0)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
fi = outPath + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
print(fi)
sim.save(fi)
return(sim)
trs = [epq.XRayTransition(epq.Element.Ag, epq.XRayTransition.LB1),
epq.XRayTransition(epq.Element.Fe, epq.XRayTransition.KB1)]
print(trs)
# create samples consisting of silver film on steel (316H) substrate
film = {}
film[1] = [ag , 0.000000020],[s316H, 0.000010] # 0.000005000 = 5 um 0.000010 = 10um Configuring multi-layers composition and thickness
film[2] = [ag , 0.000000015],[s316H, 0.000010] # 0.000000050 = 0.05 um
film[3] = [ag , 0.000000010],[s316H, 0.000010]
xtraP = {}
xtraP = {"Characteristic Accumulator":True, "Char Fluor Accumulator":True, "Brem Fluor Accumulator":True}
# outpathoutPath = "/Users/jrminter/Documents/git/dtsa2Scripts/ben-buse/out/"
xtraP.update(mc3.configureOutput(outPath))
xtraP.update(mc3.configurePhiRhoZ(1.5*range))
xtraP.update(mc3.configureEmissionImages(trs, 1.5*range, size = 512))
xtraP.update(mc3.configureTrajectoryImage(1.5*range, size = 512))
resF = {}
for fil in film:
extension = str(film[fil][0])
extension = extension.replace("[","")
extension = extension.replace("]","")
extension = extension.replace(",","")
# pathloc = 'O:\Documents\PFE_Data\Users\Charles_Younes\\041115_CarbonInSteel\\dtsa2repeat7_' + extension # Change to output folder
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))
# xp.update(mc3.configureEmissionImages(xrts,imgSzUm*1.0e-6, imgSzPx))
# xp.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
# xp.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSzPx))
# xp.update(mc3.configureVRML(nElectrons = 40))
xp.update(mc3.configureOutput(outDir))
xp.update(mc3.configureGun(beamSzNm*1.0e-9))
ts = time.time()
# first sim bare Si
spc = mc3.simulate(si, det, e0, dose, True, nTraj, True, True, xp)
spc = epq.SpectrumUtils.addNoiseToSpectrum(spc, 1.0)
spc = wrap(spc)
sName = "Si-%g-kV-%d-traj" % ( e0, nTraj)
spc.rename(sName)
res = anaConSi(spc, det, digits=2, display=False)
cI = res["C"]
siI = res["Si"]
def simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True, nTraj=100, sf=True, bf=True, iDigits=5, bVerbose=False, xtraParams={}):
"""simLineInMatrixLimScan(lin, linMat, blk, blkMat, nmLinWid, umBlock,
nmScan, nPts, trs, outDir, hdr, det, e0, lt, pc, withPoisson=True,
nTraj=nTraj, sf=True, bf=True, iDigits=5, bVerbose=False,
xtraParams={})
Simulate a line of width `nmLinWid' nm at the center of a block of
`umBlock' microns. The line is of material `lin' with a name `linMat'.
The block is of material `blk' with a name `blkMat'. We step a total
distance of nmScan across the center of the line.
We analyze an list `trs' of transitions, writing the K-ratios to a
.csv file with a header `hdr'. We use the detector `det', voltage `e0'
(kV) and live time `lt' sec and probe current `pc' nA. This will
compute the standard spectra, compute the spectra the scanned
region. It will then compute the K-ratios for each spectrum and write
them to a file `name' in outDir with a header `hdr' that matches the
transition order.
"""
# order is order of trs..
sc = 1.0e-6 # scale from microns to meters for positions
dose = lt*pc
lX = [] # an array for postions
lKlin = [] # an array for the K-ratio of the line
lKblk = [] # an array for the K-ratio of the block. Title correspond to hdr string
umLine = nmLinWid * 1.0e-3
# start clean
dt2.DataManager.clearSpectrumList()
# create the standards
linStd = simulateBulkStandard(lin, linMat, det, e0, lt, pc, withPoisson=withPoisson, nTraj=nTraj, sf=sf, bf=bf, xtraParams={})
dt2.display(linStd)
blkStd = simulateBulkStandard(blk, blkMat, det, e0, lt, pc, withPoisson=withPoisson, nTraj=nTraj, sf=sf, bf=sf, xtraParams={})
dt2.display(blkStd)
lStd = {"El":dt2.element(linMat), "Spc":linStd}
bStd = {"El":dt2.element(blkMat), "Spc":blkStd}
stds = [lStd, bStd] # note: put the transitions in this order
iCount = 0
for x in range(-nPts/2, (nPts/2)+1, 1):
xPosNm = x * nmScan / nPts
lX.append(round(xPosNm, iDigits))
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(trs, charAccum=sf, charFluorAccum=sf, bremFluorAccum=bf))
xtraParams.update(mc3.configureOutput(outDir))
xtraParams.update(mc3.configureBeam(xPosNm*1.0e-09, 0, -0.099, 1.0))
spec = mc3.embeddedRectangle(lin, [umLine*sc, umBlock*sc, umBlock*sc], blk, 0, det, e0, withPoisson=withPoisson, nTraj=nTraj, dose=dose, sf=sf, bf=bf, xtraParams=xtraParams)
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.FaradayEnd, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
spcName = "x = %.3f um" % x
epq.SpectrumUtils.rename(spec, spcName)
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
# display(spec)
a = jmg.compKRs(spec, stds, trs, det, e0)
iCount += 1
print(iCount, xPosNm)
lKlin.append(round(a[0], iDigits))
lKblk.append(round(a[1], iDigits))
basFile ="%gnm-%s-in-%gum-%s-%gkV-%g-Traj.csv" % (nmLinWid, linMat, umBlock, blkMat, e0, nTraj)
strOutFile = outDir + "/" + basFile
f=open(strOutFile, 'w')
strLine = hdr + '\n'
f.write(strLine)
for i in range(iCount):
strLine = "%.3f" % lX[i] + ","
strLine = strLine + "%.5f" % lKlin[i] + ","
strLine = strLine + "%.5f" % lKblk[i] + "\n"
f.write(strLine)
f.close()
# 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))
# xp.update(mc3.configureEmissionImages(xrts,imgSzUm*1.0e-6, imgSzPx))
# xp.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
# xp.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSzPx))
# xp.update(mc3.configureVRML(nElectrons = 40))
xp.update(mc3.configureOutput(outDir))
xp.update(mc3.configureGun(beamSzNm * 1.0e-9))
ts = time.time()
# first sim bare Si
spc = mc3.simulate(si, det, e0, dose, True, nTraj, True, True, xp)
spc = epq.SpectrumUtils.addNoiseToSpectrum(spc, 1.0)
spc = wrap(spc)
sName = "Si-%g-kV-%d-traj" % (e0, nTraj)
spc.rename(sName)
res = anaConSi(spc, det, digits=2, display=False)
cI = res["C"]
siI = res["Si"]
trs = mc3.suggestTransitions(eagleXG, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(c, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configurePhiRhoZ(przDepUm * 1.0e-6))
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSize))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(outDir))
print(xtraParams)
fmtS = "%g-nm-C-on-EagleXG-at-%g-kV"
print("Starting simulation")
multiLaySim = mc3.multiFilm(layers, det, e0, True, nTraj, dose, True, True,
xtraParams)
sName = fmtS % (tCNm, e0)
multiLaySim.rename(sName)
multiLaySim.setAsStandard(eagleXG)
multiLaySim.display()
fi = outDir + "/"
fi += sName
def fullSimBulkStd(mat, ctg, ctgThickNm, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False):
"""
fullSimBulkStd(mat, ctg, ctgThickNm, det, e0, nTraj, outPath,
dim=5.0e-6, lt=100, pc=1.0, emiSize=512, ctd=False)
Use mc3 simulation to simulate an uncoated standard specimen
Parameters
----------
mat - a dtsa material.
Note the material must have an associated density. It should
have a useful name.
ctg - a dtsa2 material for the coating
det - a dtsa detector
Here is where we get the detector properties and calibration
e0 - float
The accelerating voltage in kV
nTraj - integer
The number of trajectories to run
outPath - string
The path to the directory for output
dim - float (5.0e-6)
The size of the emission images
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
emiSize - int (default 512)
The width and depth of the emission images.
ctd - Boolean (False) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2 as dtsa2
import dtsa2.mcSimulate3 as mc3
det = findDetector("Oxford p4 05eV 4K")
cu = material("Cu", density=8.92)
outPath = "C:/Users/johnr/Documents/git/dtsa2Scripts/ben-buse/out"
a = fullSimBulkStd(cu, det, 15.0, 100, outPath,
dim=5.0e-6, lt=100,
pc=1.0, emiSize=512, ctd=False)
a.display()
"""
strCtg = ctg.getName()
strMat = mat.getName()
dose = pc * lt # na-sec"
# specify the transitions to generate
xrts = []
trs = mc3.suggestTransitions(mat, e0)
for tr in trs:
xrts.append(tr)
trs = mc3.suggestTransitions(ctg, e0)
for tr in trs:
xrts.append(tr)
# At 20 kV the images are best at 2.0e-6
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, 2.0e-6, 512))
xtraParams.update(mc3.configurePhiRhoZ(2.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(2.0e-6, 512))
xtraParams.update(mc3.configureVRML(nElectrons=100))
xtraParams.update(mc3.configureOutput(outPath))
print("Output sent to %s") % (outPath)
layers = [ [ctg, ctgThickNm*1.0e-9],
[mat, 1.0e-3]]
sim = mc3.multiFilm(layers, det, e0, withPoisson=True, nTraj=nTraj,
dose=dose, sf=True, bf=True, xtraParams=xtraParams)
sName = "%g-nm-%s-on-%s" % (tNmC, strCtg, strMat)
sim.rename(sName)
sim.setAsStandard(mat)
sim.display()
return(sim)
