xrts = []
trs = mc3.suggestTransitions(mix, e0)
for tr in trs:
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)
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 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 = 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(simDir))
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 = spcDir + "/"
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)
