def bkgStripRipple(rplDir, rplBas, e0, i0, liveTime, det, verbose=False):
"""
bkgStripRipple(rplDir, rplBas, e0, i0, liveTime, det, verbose=False)
Strip the background from a ripple file, writing the output to a
a file with -bks appended to the name.
Parameters
----------
rplDir: string (with path terminator)
The directory containing the ripple file
rplBas: string
The base name of the ripple file
e0: number
Accelerating voltage (kV)
i0: number
Probe current (nA)
liveTime: number
Llve time per pixel (sec)
det: DTSA-II detector
The detector (used to get channel depth)
verbose: Boolean (False)
Flag to print progress (row and elapsed time)
"""
start = time.time()
rplPth = rplDir + rplBas
rplFil = rplPth + ".rpl"
a1 = rplPth + "-bks.rpl"
a2 = rplPth + "-bks.raw"
sRip = openRipple(rplFil, e0, i0, liveTime, det)
cols = sRip.getColumns()
rows = sRip.getRows()
# print((cols, rows))
depth = det.getChannelCount()
res = ept.RippleFile(cols, rows, depth, ept.RippleFile.UNSIGNED , 4,
ept.RippleFile.BIG_ENDIAN, a1, a2)
for x in range(cols):
for y in range(rows):
if (y==0):
if(x>0):
now = time.time()
delta = (now-start)/60
msg = "Started row %d of %d. " % (x+1, cols)
msg += "This script required %.1f min so far" % (delta)
print(msg)
if(delta > 60):
delta = delta/60
msg = "...or %.3f hr" % delta
print(msg)
sRip.setPosition(x,y)
spc = dt2.wrap(sRip)
spc = epq.SpectrumUtils.applyZeroPeakDiscriminator(spc)
spc = epq.PeakStripping.Clayton1987.getStrippedSpectrum(spc)
spc = epq.SpectrumUtils.getPositiveSpectrum(spc)
res.seek(y, x) # think this was the problem...
res.write(epq.SpectrumUtils.toIntArray(spc)[0:depth])
res.close()
def anaMcNiCuKa(spc, det, stdBase, maxCh=1200):
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericProperty(epq.SpectrumProperties.WorkingDistance)
spc = jmg.cropSpec(spc, end=maxCh)
unSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(unSpc)
# define the transitions I want to measure
tsNiKa = epq.XRayTransitionSet(epq.Element.Ni, epq.XRayTransitionSet.K_FAMILY)
tsCuKa = epq.XRayTransitionSet(epq.Element.Cu, epq.XRayTransitionSet.K_FAMILY)
trs = [tsNiKa, tsCuKa]
relStd = "/%gkV/" % (e0)
stdDir = stdBase + relStd
niFile = stdDir + "Ni-sim.msa"
cuFile = stdDir + "Cu-sim.msa"
spc = dt2.wrap(ept.SpectrumFile.open(niFile)[0])
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericWithDefault(epq.SpectrumProperties.WorkingDistance, wkDst)
spc = jmg.cropSpec(spc, end=maxCh)
niSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(niSpc)
spc = dt2.wrap(ept.SpectrumFile.open(cuFile)[0])
props=spc.getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
lt = props.getNumericProperty(epq.SpectrumProperties.LiveTime)
pc = props.getNumericProperty(epq.SpectrumProperties.FaradayBegin)
wkDst = props.getNumericWithDefault(epq.SpectrumProperties.WorkingDistance, wkDst)
spc = jmg.cropSpec(spc, end=maxCh)
cuSpc = jmg.updateCommonSpecProps(spc, det, liveTime=lt, probeCur=pc, e0=e0, wrkDist=wkDst)
dt2.display(cuSpc)
niStd = {"El":dt2.element("Ni"), "Spc":niSpc}
cuStd = {"El":dt2.element("Cu"), "Spc":cuSpc}
stds = [niStd, cuStd]
theKR = jmg.compKRs(unSpc, stds, trs, det, e0)
krNiCalc = theKR[0]
krCuCalc = theKR[1]
return [krNiCalc, krCuCalc]
def simSonoraSpc(tAl2O3, e0, det, wkDst=5, lt=100, pc=1, nTraj=1000, xtraParams={}):
"""simSonoraSpc(tAl2O3, e0, det, wkDst=5, lt=100, pc=1, nTraj=1000, xtraParams={})
Simulate a spectrum from tAl2O3 nm of Al2O3 on Al recoreed at
e0 kV using the DTSA detector det and a wkDst mm working distance for
lt sec with a probe current of pc nA. Compute nTraj trajectories."""
tAl = 100 # um
al2o3 = dt2.material("Al2O3",density=3.95)
al = dt2.material("Al", density=2.70)
lAl2O3 = [al2o3, tAl2O3*1.0e-9]
lAl = [al, tAl*1.0e-6]
lay = [lAl2O3, lAl]
sNam = "%g-nm-Al2O3-on-Al-%g-kV" % (tAl2O3, e0)
spc = dt2.wrap(mc3.multiFilm(lay, det, e0, True, nTraj, lt*pc, True, True, xtraParams))
props=spc.getProperties()
props.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, sNam)
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
props.setNumericProperty(epq.SpectrumProperties.WorkingDistance, wkDst)
return(spc)
def simNiCuPetSpc(tNi, tCu, e0, det, wkDst=17, lt=100, pc=1, nTraj=1000):
"""simNiCuPetSpc(tNi, tCu, e0, det, wkDst=17, lt=100, pc=1, nTraj=1000)
Simulate a spectrum from tNi nm of Ni on tCu nm of Cu on PET recoreded at
e0 kV using the DTSA detector det and a wkDst mm working distance for
lt sec with a probe current of pc nA. Compute nTraj trajectories."""
tPET = 76 # um
pet = dt2.material("C10H8O4",density=1.37)
cu = dt2.material("Cu", density=8.96)
ni = dt2.material("Ni", density=8.90)
lNi = [ni, tNi*1.0e-9]
lCu = [cu, tCu*1.0e-9]
lPET = [pet, tPET*1.0e-6]
lay = [lNi, lCu, lPET]
sNam = "%g-nm-Ni-%g-nm-Cu-on-PET-%g-kV" % (tNi, tCu, e0)
spc = dt2.wrap(mc3.multiFilm(lay, det, e0, True, nTraj, lt*pc, True, True))
props=spc.getProperties()
props.setTextProperty(epq.SpectrumProperties.SpectrumDisplayName, sNam)
props.setNumericProperty(epq.SpectrumProperties.LiveTime, lt)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, pc)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
props.setNumericProperty(epq.SpectrumProperties.WorkingDistance, wkDst)
return(spc)
def buildVectors(stds, path=None, strip=(), det=None):
"""buildVectors(stds, path=None,strip=())
Construct a set of Schamber-style fast quant vectors
stds = { "Fe" : "Fe std", "Cr": "Cr std", "Cd":s101 ... }
path = "/home/nicholas/standards" or similar (None -> defaultPath)
strip= ("C", "O", ...) a list of elements to strip (must also be in stds)"""
procStds = {}
strip = [element(elm) for elm in strip]
e0 = None
for elm, std in stds.iteritems():
if isinstance(std, str):
path = (path if path else defaultVecPath)
std = readSpectrum("%s/%s" % (path, std))
elif isinstance(std, dt2.ScriptableSpectrum):
std = std.wrapped
det = (det if det else std.getProperties().detector)
procStds[dt2.element(elm)] = std
e0 = (e0 if e0 else epq.ToSI.keV(dt2.wrap(std).beamEnergy()))
sv = fq.SchamberVectors(det, e0)
for elm, std in procStds.iteritems():
sv.addStandard(elm, std, elm in strip)
return sv.getVectorSet()
def base(det, e0, withPoisson, nTraj, dose, sf, bf, name, buildSample, buildParams, xtraParams):
"""base(det, e0, withPoisson, nTraj, dose, sf, bf, name, buildSample, buildParams) represents \
a generic mechanism for Monte Carlo simulation of x-ray spectra. The argument buildSample \
is a method buildSample(monte,origin,buildParams) taking an instance of MonteCarloSS, the \
position of the origin and a dictionary of build parameters. This method should construct \
the sample geometry. The other arguments are the detector, the beam energy (keV), whether \
to add Poisson noise, the number of electron trajectories to simulate, whether to simulate \
characteristic secondary fluorescence and Bremsstrahlung secondary fluorescence, the name \
to assign to the resulting spectrum."""
if e0 < 0.1:
raise "The beam energy must be larger than 0.1 keV."
if nTraj < 1:
raise "The number of electron trajectories must be larger than or equal to 1."
if dose <= 0.0:
raise "The electron dose must be larger than zero."
name = name.strip()
if xtraParams.has_key("Postfix"):
name = "%s - %s" % (name, xtraParams["Postfix"])
# Place the sample at the optimal location for the detector
origin = epq.SpectrumUtils.getSamplePosition(det.getProperties())
# Create a simulator and initialize it
monte = nm.MonteCarloSS()
if xtraParams.has_key("Gun"):
gun = xtraParams["Gun"]
gun.setCenter([0.0, 0.0, -0.099])
monte.setElectronGun(gun)
if xtraParams.has_key("PosX"):
beamX = xtraParams["PosX"]
beamY = xtraParams["PosY"]
beamZ = xtraParams["PosZ"]
beamNM = xtraParams["nmSize"]
beam=nm.GaussianBeam(beamNM*1.0e-9)
beam.setCenter([beamX, beamY, beamZ])
monte.setElectronGun(beam)
chamber = monte.getChamber()
if xtraParams.has_key("VP"):
pathLength, gas = xtraParams["VP"]
dim = 0.5 * nm.MonteCarloSS.ChamberRadius;
dims = epu.Math2.plus(epu.Math2.v3(dim, dim, dim), epu.Math2.z3(2.0 * pathLength))
pt = epu.Math2.plus(origin, epu.Math2.z3(0.5 * dim));
shape = nm.MultiPlaneShape.createBlock(dims, pt, 0.0, 0.0, 0.0);
msm = nm.BasicMaterialModel(gas);
chamber = monte.addSubRegion(chamber, msm, shape);
monte.setBeamEnergy(epq.ToSI.keV(e0))
buildSample(monte, chamber, origin, buildParams)
# Add event listeners to model characteristic radiation
chXR = nm3.CharacteristicXRayGeneration3.create(monte)
xrel = nm3.XRayTransport3.create(monte, det, chXR)
brXR = nm3.BremsstrahlungXRayGeneration3.create(monte)
brem = nm3.XRayTransport3.create(monte, det, brXR)
chSF, brSF, bremFluor, charFluor = None, None, None, None
hasCharAcc = xtraParams.has_key('Characteristic Accumulator') and xtraParams['Characteristic Accumulator']
if sf or hasCharAcc or xtraParams.has_key("Compton"):
charFluor = nm3.FluorescenceXRayGeneration3.create(monte, chXR)
if xtraParams.has_key("Compton"):
charFluor.setIncludeCompton(True)
chSF = nm3.XRayTransport3.create(monte, det, charFluor)
hasBremFluorAcc = xtraParams.has_key('Brem Fluor Accumulator') and xtraParams['Brem Fluor Accumulator']
if bf or hasBremFluorAcc:
bremFluor = nm3.FluorescenceXRayGeneration3.create(monte, brXR)
brSF = nm3.XRayTransport3.create(monte, det, bremFluor)
hasTrans = xtraParams.has_key("Transitions")
if hasTrans:
if xtraParams.has_key("Emission Images"):
eis = []
dim = xtraParams["Emission Images"]
for xrt in xtraParams["Transitions"]:
size = xtraParams["Emission Size"]
ei = nm3.EmissionImage3(size, size, xrt)
xrel.addXRayListener(ei)
if chSF:
chSF.addXRayListener(ei)
if brSF:
brSF.addXRayListener(ei)
ei.setXRange(origin[0] - 0.5 * dim, origin[0] + 0.5 * dim)
ei.setYRange(origin[2] - 0.1 * dim, origin[2] + 0.9 * dim)
eis.append(ei)
if hasCharAcc:
cxra = nm3.XRayAccumulator3(xtraParams["Transitions"], "Characteristic", dose * 1.0e-9)
xrel.addXRayListener(cxra)
hasCharFluorAcc = xtraParams.has_key('Char Fluor Accumulator') and xtraParams['Char Fluor Accumulator']
if hasCharFluorAcc or chSF or sf:
cfxra = nm3.XRayAccumulator3(xtraParams["Transitions"], "Characteristic Fluorescence", dose * 1.0e-9)
chSF.addXRayListener(cfxra)
if hasBremFluorAcc or brSF or bf:
bfxra = nm3.XRayAccumulator3(xtraParams["Transitions"], "Continuum Fluorescence", dose * 1.0e-9)
brSF.addXRayListener(bfxra)
contImgs = []
if xtraParams.has_key('Continuum Images'):
dim = xtraParams['Continuum Images']
size = xtraParams['Continuum Size']
energies = xtraParams['Continuum Energies']
for eMin, eMax in energies:
ci3 = nm3.ContinuumImage3(size, size, epq.ToSI.keV(eMin), epq.ToSI.keV(eMax))
ci3.setXRange(origin[0] - 0.5 * dim, origin[0] + 0.5 * dim)
ci3.setYRange(origin[2] - 0.1 * dim, origin[2] + 0.9 * dim)
brem.addXRayListener(ci3)
contImgs.append(ci3)
doPRZ = xtraParams.has_key("PhiRhoZ")
if doPRZ:
depth = xtraParams["PhiRhoZ"]
prz = nm3.PhiRhoZ3(xrel, origin[2] - 0.1 * depth, origin[2] + 1.1 * depth, 110)
xrel.addXRayListener(prz)
voxelated = xtraParams.has_key('Voxelated')
vox = None
if voxelated:
dim = xtraParams['Voxelated']
gen = xtraParams['GeneratedV']
size = xtraParams['SizeV']
vox = nm3.VoxelatedDetector((origin[0], origin[1], origin[2] - 0.1 * size), (size, size, size), (dim, dim, dim), gen)
xrel.addXRayListener(vox)
doTraj = xtraParams.has_key('Trajectories')
if doTraj:
dim = xtraParams['Trajectories']
size = xtraParams['TrajSize']
ti = nm.TrajectoryImage(size, size, dim)
ti.setXRange(origin[0] - 0.5 * dim, origin[0] + 0.5 * dim)
ti.setYRange(origin[2] - 0.1 * dim, origin[2] + 0.9 * dim)
monte.addActionListener(ti)
defOut = (dtsa2.DefaultOutput if dtsa2.DefaultOutput else dtsa2.reportPath())
do = ("%s\\%s" % (xtraParams["Output"], dtsa2.normalizeFilename(name)) if xtraParams.has_key("Output") else "%s/%s" % (defOut, dtsa2.normalizeFilename(name)))
do = do.replace("\\", "/")
fdo = jio.File(do)
fdo.mkdirs()
doVRML = xtraParams.has_key('VRML')
vrmlWr = None
if doVRML:
vrmlFile = jio.File.createTempFile("vrml", ".wrl", fdo)
print "VRML in " + str(vrmlFile)
vrmlWr = jio.FileWriter(vrmlFile)
vrml = nm.TrajectoryVRML(monte, vrmlWr)
vrml.setDisplayBackscatter(False)
vrml.setDisplayXRayEvent(True)
vrml.setMaxTrajectories(xtraParams['VRML'])
vrml.setTrajectoryWidth(1.0e-9)
vrml.setMaxRadius(1.0)
vrml.setEmissive(True)
vrml.addView("Y-Axis", epu.Math2.plus(origin, (0.0, 5.0e-6, 0.0)), origin)
vrml.addView("Gun", epu.Math2.plus(origin, (0.0, 0.0, -5.0e-6)), origin)
vrml.addView("X-Axis", epu.Math2.plus(origin, (-5.0e-6, 0.0, 0.0)), origin)
vrml.renderSample()
monte.addActionListener(vrml)
scatter = None
if xtraParams.has_key("Scatter"):
scatter = nm.ScatterStats(epq.ToSI.eV(50.0))
monte.addActionListener(scatter)
# Reset the detector and run the electrons
det.reset()
monte.runMultipleTrajectories(nTraj)
# Get the spectrum and assign properties
spec = det.getSpectrum((dose * 1.0e-9) / (nTraj * epq.PhysicalConstants.ElectronCharge))
props = spec.getProperties()
props.setNumericProperty(epq.SpectrumProperties.LiveTime, dose)
props.setNumericProperty(epq.SpectrumProperties.FaradayBegin, 1.0)
props.setNumericProperty(epq.SpectrumProperties.BeamEnergy, e0)
epq.SpectrumUtils.rename(spec, name)
if withPoisson:
spec = epq.SpectrumUtils.addNoiseToSpectrum(spec, 1.0)
printAcc = xtraParams.has_key('Print Accumulators') and xtraParams['Print Accumulators']
if printAcc:
sw0 = jio.StringWriter()
sw = jio.PrintWriter(sw0)
if hasTrans or scatter:
pw = None
if hasCharAcc or (hasBremFluorAcc and bf) or (hasCharFluorAcc and sf) or scatter:
jio.File(do).mkdirs()
pw = jio.PrintWriter("%s/Intensity.csv" % do)
pw.println(name)
if hasCharAcc:
pw.println("Characteristic")
cxra.dump(pw)
if printAcc:
sw.println("Characteristic")
cxra.dump(sw)
if hasBremFluorAcc and brSF and bf:
pw.println("Bremsstrahlung Fluorescence")
bfxra.dump(pw)
if printAcc:
sw.println("Bremsstrahlung Fluorescence")
bfxra.dump(sw)
if hasCharFluorAcc and chSF and sf:
pw.println("Characteristic Fluorescence")
cfxra.dump(pw)
if printAcc:
sw.println("Characteristic Fluorescence")
cfxra.dump(sw)
if printAcc:
print sw0.toString()
sw.close()
sw0.close()
if scatter:
scatter.header(pw)
scatter.dump(pw)
if pw:
pw.close()
imgs = []
if xtraParams.has_key("Emission Images"):
nm3.EmissionImageBase.scaleEmissionImages(eis)
print eis
print do
nm3.EmissionImage3.dumpToFiles(eis, do)
print u"Writing emission images to %s" % do
imgs.extend(eis)
if xtraParams.has_key("Continuum Images"):
imgs.extend(contImgs)
nm3.EmissionImageBase.scaleEmissionImages(imgs)
print contImgs
print do
nm3.ContinuumImage3.dumpToFiles(contImgs, do)
print u"Writing continuum images to %s" % do
if doPRZ:
jio.File(do).mkdirs()
pw = jio.PrintWriter(u"%s/PhiRhoZ.csv" % do)
prz.write(pw)
pw.close()
print u"Writing emission images to %s" % do
if doTraj:
ti.dumpToFile(do)
print u"Writing trajectory images to %s" % do
if vrmlWr:
vrmlWr.close()
if vox:
jio.File(do).mkdirs()
objs = list(vox.getAccumulatorObjects())
xx = {}
for obj in objs:
iio.write(vox.createXZSum(400, obj), "png", jio.File(do, "Voxelated[XZ,Sum][%s].png" % obj))
iio.write(vox.createXYSum(400, obj), "png", jio.File(do, "Voxelated[XY,Sum][%s].png" % obj))
iio.write(vox.createXZView(400, obj), "png", jio.File(do, "Voxelated[XZ, Max][%s].png" % obj))
iio.write(vox.createXYView(400, obj), "png", jio.File(do, "Voxelated[XY, Max][%s].png" % obj))
vox.writeXZPlanar(400, obj, jio.File(do, "Voxilated[XZ,planar,%s].tif" % obj))
vox.writeXYPlanar(400, obj, jio.File(do, "Voxilated[XY,planar,%s].tif" % obj))
for f in (0.1, 0.5, 0.8, 0.9):
iio.write(vox.createXZFraction(400, obj, f), "png", jio.File(do, "Voxelated[XZ,f=%g][%s].png" % (f, obj)))
xx[obj] = vox.createRadialCDF(origin, obj)
hdr = "Radius"
for obj in objs:
hdr = "%s\t%s" % (hdr, obj)
print hdr
first = xx[objs[0]]
for i, (d, f) in enumerate(first):
ln = "%g" % d
for obj in objs:
rcdf = xx[obj][i]
ln = "%s\t%g" % (ln, rcdf[1])
print ln
#if bremFluor:
#print "Stats[Scale] = %s" % bremFluor.getScaleStats()
return dtsa2.wrap(spec)
