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 simulateBulkStandard(mat,
name,
det,
e0,
lt,
pc,
withPoisson=True,
nTraj=100,
sf=True,
bf=True,
xtraParams={}):
"""simulateBulkStandard(mat, name, det, e0, lt, pc, withPoisson=True,
nTraj=100, sf=True, bf=True, xtraParams={})"""
std = mc3.simulate(mat,
det,
e0,
lt * pc,
withPoisson=True,
nTraj=nTraj,
sf=True,
bf=True,
xtraParams={})
props = std.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)
std.setAsStandard(mat)
return (std)
def simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0, ctd=True):
"""simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0)
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
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
ctd - Boolean (True) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = jm3.simBulkStd(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)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
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)
return sim
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 simulateBulkStandard(mat, name, det, e0, lt, pc, withPoisson=True, nTraj=100, sf=True, bf=True, xtraParams={}):
"""simulateBulkStandard(mat, name, det, e0, lt, pc, withPoisson=True,
nTraj=100, sf=True, bf=True, xtraParams={})"""
std = mc3.simulate(mat, det, e0, lt*pc, withPoisson=True, nTraj=nTraj, sf=True, bf=True, xtraParams={})
props=std.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)
std.setAsStandard(mat)
return(std)
def simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0, ctd=True):
"""simBulkStd(mat, det, e0, nTraj, lt=100, pc=1.0)
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
lt - integer (100)
The live time (sec)
pc - float (1.0)
The probe current in nA
ctd - Boolean (True) - is C coated
Returns
-------
sim - DTSA scriptable spectrum
The simulated standard spectrum
Example
-------
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 2K")
cu = material("Cu", density=8.92)
a = jm3.simBulkStd(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)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
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)
return sim
def simulate_spectrum(mat, e0, det, nTraj, dose, spcDir):
"""
simulate_spectrum(mat, e0, det, nTraj, dose, spcDir)
"""
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)
sName = "%s std-%g-kV" % (mat.getName(), e0)
spc.rename(sName)
spc.setAsStandard(mat)
spc.display()
# Save the spectra if NTraj > 500
if nTraj > 500:
fi = spcDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc.save(fi)
return (spc)
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)
DataManager.clearSpectrumList()
start = time.time()
zno = material("ZnO", density=5.61)
si = material("Si", density=2.33)
xrts = []
trs = mc3.suggestTransitions(zno, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts,True, True, True))
# xtraParams.update(mc3.configureOutput(simDir))
spc_zno_std = mc3.simulate(zno, det, e0, dose, True, nTraj, True, True, xtraParams)
sName = "ZnO std-%g-kV" % (e0)
spc_zno_std.rename(sName)
spc_zno_std.setAsStandard(zno)
spc_zno_std.display()
fi = resDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc_zno_std.save(fi)
xrts = []
trs = mc3.suggestTransitions(si, e0)
for tr in trs:
xrts.append(tr)
xtraParams={}
start = time.time()
homDir = os.environ['HOME']
homDir = homDir.replace('\\', '/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/utility/output/"
rptDir = wrkDir + '/test-mc3-simulate-Al Results/'
DataManager.clearSpectrumList()
e0 = 15.0
det = findDetector("Probe")
mat = material("Al", 2.7)
spc = mc3.simulate(mat, det, e0, 120.0, True, 10000, True, True, {})
sName = "Bulk Al"
spc.rename(sName)
spc.display()
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
xrts.append(tr)
# print(xrts)
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(simDir))
print(xtraParams)
sim = mc3.simulate(mix, det, e0, dose, True, nTraj, True, True, xtraParams)
fmtS = "Admiralty-Brass-at-%g-kV"
sName = fmtS % (e0)
sim.rename(sName)
sim.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
sim.save(fi)
# clean up cruft
shutil.rmtree(rptDir)
print "Done!"
end = time.time()
delta = (end - start) / 60
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/mc3Scripts"
prjDir = gitHom + relPrj
datDir = prjDir + "/dat"
simDir = datDir + "/sim"
jmg.ensureDir(datDir)
jmg.ensureDir(simDir)
os.chdir(prjDir)
pyrDir = prjDir + "/mc3Bulk Results"
xrts = [transition("Fe K-L3"), transition("Fe K-M3"), transition("Fe L3-M5"), transition("O K-L3")]
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=True, charFluorAccum=True, bremFluorAccum=True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSizePx))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(material("Fe2O3",5.0), det, e0, dose = pc*lt, nTraj=nTraj, sf=True, bf=True, xtraParams = xtraParams)
display(spc)
shutil.rmtree(pyrDir)
print "Done!"
# mc3SimulateBaTiO3.py
#
# Simulate a bulk barium titanante spectrum. This is as simple as it
# gets.
#
# Date Ver Who Notes
# 2015-05-21 0.90 JRM Initial example. Verified with Iona v.2015-05-01
#
import dtsa2.mcSimulate3 as mc3
det = findDetector("Probe") # DTSA-II default detector, use yours
e0 = 15 # keV
nTraj = 1000 # electrons
dose = 150 # nA*sec
withPoisson = True # Add Poisson noise
sf = True # Secondary Florescence
bf = True # Brehmstrahlung Florescence
mat = epq.Material(
epq.Composition([epq.Element.Ba, epq.Element.Ti, epq.Element.O],
[0.2058, 0.2053, 0.5889]), epq.ToSI.gPerCC(6.02))
mat.setName("BaTiO3")
spc = mc3.simulate(mat, det, e0, dose, withPoisson,
nTraj) # sf=False, bf=False, xtraParams={})
display(spc)
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)
dose = pc * lt # nA sec
DataManager.clearSpectrumList()
b = material("B", density=2.37)
bn = material("BN", density=2.1)
aln = material("AlN", density=3.26)
# Sim B
xrts = [transition("B K-L2"), transition("B K-L3")]
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=True, charFluorAccum=True, bremFluorAccum=True))
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSizePx))
xtraParams.update(mc3.configureVRML(nElectrons = vmrlEl))
xtraParams.update(mc3.configureOutput(spcDir))
b_spc = mc3.simulate(b, det, e0, dose = pc*lt, nTraj=nTraj, sf=True, bf=True, xtraParams = xtraParams)
b_spc.rename("B")
# b_spec.setAsStandard(b)
display(b_spc)
fi = spcDir + "/B-%g-kV-%g-Traj.msa" % (e0, nTraj)
b_spc.save(fi)
# Sim BN
xrts = [transition("B K-L2"), transition("B K-L3"),
transition("N K-L2"), transition("N K-L3")]
xtraParams={}
xtraParams.update(mc3.configureXRayAccumulators(xrts, charAccum=True, charFluorAccum=True, bremFluorAccum=True))
#
# note that the image size on the specimen is in meters...
xtraParams.update(mc3.configureEmissionImages(xrts, imgSzUm*1.0e-6, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm*1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm*1.0e-6, imgSizePx))
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"]
lT.append(0.0)
lPICmu.append(cI[0])
lPICuc.append(cI[1])
lPISimu.append(siI[0])
lPISiuc.append(siI[1])
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/utility/output/"
rptDir = wrkDir + '/test-mc3-simulate-Fe2O3/'
# Note: On Win10 MSA files are in:
# C:\Users\johnr\Documents\git\dtsa2scripts\utility\output
bSaveSpc = True
DataManager.clearSpectrumList()
e0 = 20.0 # or 5.0
nTraj = 10000
det = findDetector("Oxford p4 05eV 4K")
mat = material("Fe2O3", 5.0)
spc = mc3.simulate(mat, det, e0, 120.0, True, nTraj, True, True, {})
sName = "Bulk Fe2O3"
spc.rename(sName)
spc.display()
fi = outDir + "/Fe2O3-%g-kV-%g-Traj.msa" % (e0, nTraj)
spc.save(fi)
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
transition("O K-L3")
]
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=True,
charFluorAccum=True,
bremFluorAccum=True))
# note that the image size on the specimen is in meters...
xtraParams.update(
mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm * 1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSizePx))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(simDir))
spc = mc3.simulate(material("Fe2O3", 5.0),
det,
e0,
dose=pc * lt,
nTraj=nTraj,
sf=True,
bf=True,
xtraParams=xtraParams)
display(spc)
shutil.rmtree(pyrDir)
print "Done!"
b = material("B", density=2.37)
# bn = material("BN", density=2.1)
# aln = material("AlN", density=3.26)
# Sim B
xrts = [transition("B K-L2"), transition("B K-L3")]
xtraParams = {}
xtraParams.update(
mc3.configureXRayAccumulators(xrts,
charAccum=True,
charFluorAccum=True,
bremFluorAccum=True))
# note that the image size on the specimen is in meters...
xtraParams.update(
mc3.configureEmissionImages(xrts, imgSzUm * 1.0e-6, imgSizePx))
xtraParams.update(mc3.configurePhiRhoZ(imgSzUm * 1.0e-6))
xtraParams.update(mc3.configureTrajectoryImage(imgSzUm * 1.0e-6, imgSizePx))
xtraParams.update(mc3.configureVRML(nElectrons=vmrlEl))
xtraParams.update(mc3.configureOutput(spcDir))
b_spc = mc3.simulate(b, det, e0, dose, nTraj, True, True, xtraParams)
b_spc.rename("B")
b_spc.setAsStandard(b)
display(b_spc)
fi = spcDir + "/B-%g-kV-%g-Traj.msa" % (e0, nTraj)
b_spc.save(fi)
end = time.time()
delta = end - start
print(delta)
DataManager.clearSpectrumList()
start = time.time()
zno = material("ZnO", density=5.61)
si = material("Si", density=2.33)
xrts = []
trs = mc3.suggestTransitions(zno, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# xtraParams.update(mc3.configureOutput(simDir))
spc_zno_std = mc3.simulate(zno, det, e0, dose, True, nTraj, True, True,
xtraParams)
sName = "ZnO std-%g-kV" % (e0)
spc_zno_std.rename(sName)
spc_zno_std.setAsStandard(zno)
spc_zno_std.display()
fi = resDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
spc_zno_std.save(fi)
xrts = []
trs = mc3.suggestTransitions(si, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
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"]
lT.append(0.0)
lPICmu.append(cI[0])
lPICuc.append(cI[1])
lPISimu.append(siI[0])
lPISiuc.append(siI[1])
start = time.time()
homDir = os.environ['HOME']
homDir = homDir.replace('\\','/')
wrkDir = homDir + "/Documents/git/dtsa2Scripts/utility"
outDir = homDir + "/Documents/git/dtsa2Scripts/utility/output/"
rptDir = wrkDir + '/test-mc3-simulate-Al Results/'
DataManager.clearSpectrumList()
e0 = 15.0
det = findDetector("Probe")
mat = material("Al", 2.7)
spc = mc3.simulate(mat, det, e0, 120.0, True, 10000, True, True, {})
sName = "Bulk Al"
spc.rename(sName)
spc.display()
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
# mc3SimulateBaTiO3.py
#
# Simulate a bulk barium titanante spectrum. This is as simple as it
# gets.
#
# Date Ver Who Notes
# 2015-05-21 0.90 JRM Initial example. Verified with Iona v.2015-05-01
#
import dtsa2.mcSimulate3 as mc3
det = findDetector("Probe") # DTSA-II default detector, use yours
e0 = 15 # keV
nTraj = 1000 # electrons
dose = 150 # nA*sec
withPoisson = True # Add Poisson noise
sf = True # Secondary Florescence
bf = True # Brehmstrahlung Florescence
mat = epq.Material(epq.Composition([epq.Element.Ba, epq.Element.Ti, epq.Element.O],
[0.2058, 0.2053, 0.5889] ),
epq.ToSI.gPerCC(6.02))
mat.setName("BaTiO3")
spc = mc3.simulate(mat, det, e0, dose, withPoisson, nTraj) # sf=False, bf=False, xtraParams={})
display(spc)
# print(xrts)
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(simDir))
print(xtraParams)
sim = mc3.simulate(mix, det, e0, dose, True,
nTraj, True, True, xtraParams)
fmtS = "Admiralty-Brass-at-%g-kV"
sName = fmtS % (e0)
sim.rename(sName)
sim.display()
fi = simDir + "/"
fi += sName
fi += "-%g-Traj.msa" % (nTraj)
sim.save(fi)
# clean up cruft
shutil.rmtree(rptDir)
print "Done!"
lDoseUnk = [50, 100, 200, 500, 1000, 2500, 5000]
xrts = []
trs = mc3.suggestTransitions(sio2, e0)
for tr in trs:
xrts.append(tr)
xtraParams = {}
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
# xtraParams.update(mc3.configureOutput(simDir))
print(xtraParams)
spc_sio2_std = mc3.simulate(sio2, det, e0, doseStd, True, nTrajStd, True, True,
xtraParams)
sName = "SiO2 std"
spc_sio2_std.rename(sName)
spc_sio2_std.setAsStandard(sio2)
spc_sio2_std.display()
stds = {element("O"): spc_sio2_std, element("Si"): spc_sio2_std}
# oStd = {"El":element("O"), "Spc":spc_sio2_std}
#
# stds = [oStd, siStd]
for doseUnk in lDoseUnk:
spc_sio = mc3.simulate(sio, det, e0, doseUnk, True, nTrajStd, True, True,
xtraParams)
sName = "SiO Unk %g nA-sec" % (doseUnk)
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] }
res = {}
for unk in unks:
res[unk]=quantify(unk, stds, preferred = ( "Au L3-M5", "Cu K-L3" ))
tabulate(unks)
# Finally output analytical model phi(rho z) curves for comparison
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,
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}
e0 = 7.0 # keV
dose = pc * lt # nA sec
# start clean
DataManager.clearSpectrumList()
# create the materials
c = material("C", density=2.25)
cu = material("Cu", density=8.96)
trs = [epq.XRayTransitionSet(epq.Element.C, epq.XRayTransitionSet.K_FAMILY),
epq.XRayTransitionSet(epq.Element.Cu, epq.XRayTransitionSet.L_FAMILY)]
# start with bulk standards
cSpc = mc3.simulate(c, det, e0=e0, dose=dose, withPoisson=True, nTraj=nTraj, sf=charF, bf=bremF, xtraParams={})
sp=cSpc.getProperties()
sp.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName,"C-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.C))
# display(cSpc)
cStd = {"El":element("C"), "Spc":cSpc}
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)
sp.setNumericProperty(epq.SpectrumProperties.FaradayBegin, dose)
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,
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}
