e0 = 15.0 # keV
imgSize = 512 # pixel size for images
imgSzUm = 5.0 # image size in microns
vmrlEl = 250 # number of el for VMRL
dose = pc * lt # nA sec
title = "%g-um-Al2O3-on-%g-um-Ag-on-PET-%gkV" % (tFlm, tBlk, e0)
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/mc3Scripts"
prjDir = gitDir + relPrj
datDir = prjDir + "/dat"
simDir = datDir + "/sim"
csvDir = datDir + "/csv"
msaDir = datDir + "/msa"
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))
bremF = True # include continuum fluorescence
pc = 2.5 # nA
lt = 100.0 # sec
e0 = 15.0 # 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
title = "%gnmPd-%gnm-Cu-%gnm-Ag-on-PET-%gkV" % (tNmPd, tNmCu, tNmAg, e0)
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/sim-bilayer-on-sub"
datDir = gitDir + relPrj + "/msa"
csvDir = gitDir + relPrj + "/csv"
simDir = gitDir + relPrj + "/"
jmg.ensureDir(simDir)
jmg.ensureDir(datDir)
wd = gitDir + relPrj + "/py"
os.chdir(wd)
pyrDir = wd + "/sim-trilayer-on-sub Results"
det = findDetector("Oxford p4 05eV 2K")
print(det)
if 'defaultXtraParams' not in globals():
defaultXtraParams = {}
if 'defaultBremFluor' not in globals():
defaultBremFluor = False
if 'defaultCharFluor' not in globals():
defaultCharFluor = False
out = { "C": (round(cInt[0]/dose, digits), round(cInt[1]/dose, digits)),
"Si": (round(siInt[0]/dose, digits), round(siInt[1]/dose, digits))
}
return out
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/mc3Scripts"
prjDir = gitHom + relPrj
datDir = prjDir + "/dat"
csvDir = datDir + "/csv"
jmg.ensureDir(datDir)
jmg.ensureDir(csvDir)
os.chdir(prjDir)
rptDir = prjDir + '/simulate-C-on-Si Results/'
det = findDetector("Oxford p4 05eV 2K")
e0 = 5 # kV
nTraj = 10000 # trajectories
lt = 100 # sec
pc = 0.25 # nA
tNmStepC = 10
tNmCMax = 100
e0 = 15.0 # keV
imgSize = 512 # pixel size for images
imgSzUm = 5.0 # image size in microns
vmrlEl = 250 # number of el for VMRL
dose = pc * lt # nA sec
title = "%g-um-Al2O3-on-%g-um-Ag-on-PET-%gkV" % (tFlm, tBlk, e0)
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/mc3Scripts"
prjDir = gitDir + relPrj
datDir = prjDir + "/dat"
simDir = datDir + "/sim"
csvDir = datDir + "/csv"
msaDir = datDir + "/msa"
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))
import java.util as jutil
import java.io as jio
import java.nio.charset as cs
import string
start = time.time()
homDir = os.environ['HOME']
homDir = homDir.replace('\\', '/')
rPrjDir = "/Documents/git/dtsa2Scripts"
relIn = rPrjDir + "/utility"
relOut = rPrjDir + "/sim-Eagle-XG"
inDir = homDir + relIn
outDir = homDir + relOut
jmg.ensureDir(outDir)
rptDir = inDir + '/sim-C-ctd-CorningEagleXG-15kV Results/'
spcDir = outDir + "/sim"
simDir = outDir + "/sim"
jmg.ensureDir(spcDir)
jmg.ensureDir(simDir)
bVerbose = False
det = findDetector("Oxford p4 05eV 4K")
e0 = 15.0 # kV
nTraj = 200 # trajectories
lt = 100 # sec
pc = 5.0 # nA
imgSize = 512 # pixel size for images
import shutil
import time
import java.util as jutil
import java.io as jio
import java.nio.charset as cs
import string
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts"
prjDir = gitHom + relPrj
wrkDir = prjDir + "/mc3Scripts"
csvDir = wrkDir + "/dat/csv"
jmg.ensureDir(wrkDir)
os.chdir(wrkDir)
rptDir = wrkDir + '/simulateCoatedSiO2 Results/'
spcDir = wrkDir + "/dat/spc"
jmg.ensureDir(spcDir)
det = findDetector("Oxford p4 05eV 2K")
e0 = 5 # kV
nTraj = 10000 # trajectories
lt = 60 # sec
pc = 0.25 # nA
tNmTa = 2
tNmC = 10
import glob import math import shutil import time import java.io as jio import dtsa2.jmGen as jmg edsDir = os.environ['EDS_ROOT'] relDir = "/Oxford/2014-09-12-Cu-Si" wd = edsDir + relDir + "/py" os.chdir(wd) pyrDir="./anaCu5eV2K Results" datDir = edsDir + relDir + "/reports" spcDir = datDir + "/Cu-pt6-5eV-2K" rptDir = datDir + "/csv" jmg.ensureDir(rptDir) rptFil = rptDir + "/cps-per-nA-CuL-Oxford-p6-05eV-2K.csv" sDet = "Oxford p6 05eV 2K" det = findDetector(sDet) wrkDist = 5.0 # mm stdBas = datDir + "/stds" jmg.ensureDir(stdBas) stdBas = stdBas + "/" + sDet jmg.ensureDir(stdBas) lE0 = [5 , 7 , 10 , 15 , 20 , 30] lPc = [0.46, 0.60, 0.72, 0.83, 0.78, 0.78]
e0 = 4.0
det = findDetector("Oxford p4 05eV 2K")
lThNm = [
0.1, 5.0, 10.0, 20.0, 30.0, 40.0, 50.0, 60.0, 70.0, 80.0, 90.0, 100.0,
110.0, 115.0, 120.0, 125.0, 130.0, 135.0, 140.0, 145.0, 150.0
]
nTraj = 50000 # trajectories
dose = 5000 # nA-sec
nDigits = 6
# directories
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/utility"
prjDir = gitDir + relPrj
resDir = prjDir + '/sim-zno-on-si-4kV'
jmg.ensureDir(resDir)
rptDir = prjDir + '/sim-zno-on-si-4kV Results/'
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))
import time
import java.util as jutil
import java.io as jio
import java.nio.charset as cs
import string
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts"
prjDir = gitHom + relPrj
wrkDir = prjDir + "/sim-k496"
jmg.ensureDir(wrkDir)
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")
lt = 100 # spectrum live time (sec)
detNam = "Oxford p4 05eV 2K" # detector name
imgSzPx = 512
imgSzUm = 2.0
beamSzNm = 1.0
tNmMaxC = 100
tNmStepC = 2
homDir = os.environ['GIT_HOME']
relDir = "/dtsa2Scripts/estThickC"
inDir = homDir + relDir + "/py/dtsa2"
outDir = homDir + relDir + "/dat/csv"
jmg.ensureDir(outDir)
rptDir = inDir + '/simCarbonOnSi Results/'
def anaConSi(spc, det, digits=2, display=False):
"""anaConSi
Strip continuum and analyze a spectrum for C, on CuL
Parameters
----------
spc: A DTSA-II scriptable spectrum
The spectrum to process
det: The detector
out = { "C": (round(cInt[0]/dose, digits), round(cInt[1]/dose, digits)),
"Si": (round(siInt[0]/dose, digits), round(siInt[1]/dose, digits))
}
return out
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts"
prjDir = gitHom + relPrj
wrkDir = prjDir + "/mc3Scripts"
spcDir = prjDir + "/spc/Sirion/Oxford-P4-05eV-2K/Si-Cal-5kV"
csvDir = wrkDir + "/dat/csv"
jmg.ensureDir(wrkDir)
os.chdir(wrkDir)
rptDir = wrkDir + '/analyze-C-on-Si-spc Results/'
det = findDetector("Oxford p4 05eV 2K")
e0 = 5 # kV
DataManager.clearSpectrumList()
lPICmu = [] # an array for mean C peak integral
lPICuc = [] # an array for C peak integral uncertainty
lPISimu = [] # an array for mean Si peak integral
lPISiuc = [] # an array for Si peak integral uncertainty
import time
import datetime
det = findDetector("Oxford p4 05eV 2K")
e0 = 10 # kV
nTraj = 10000 # trajectories
lt = 500 # sec
pc = 5.0 # nA
dose = pc * lt # na-sec"
bSaveSpc = True
bVerbose = False
lNmCsim = [5.0, 10.0, 15.0, 20.0, 22.0, 25.0, 30.0, 35.0, 40.0]
basePath = "C:/Users/johnr/Documents/git/dtsa2scripts/sim-multilayer-calc-KRs/"
jmg.ensureDir(basePath)
csvFil = basePath + "/dtsa2-C-on-Fe3C-%g-kV-kratios-%g-traj.csv" % (e0, nTraj)
def sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0):
"""sim_amc_coated_mat(mat, det, e0, nTraj, lt=100, pc=1.0, tc=20.0)
Use mc3 multilayer simulation to simulate an am-C-ctd 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
pc = 1.0 # probe current (nA)
lt = 100 # spectrum live time (sec)
detNam = "Oxford p4 05eV 2K" # detector name
imgSzPx = 512
imgSzUm = 2.0
beamSzNm = 1.0
tNmMaxC = 100
tNmStepC = 2
homDir = os.environ['GIT_HOME']
relDir = "/dtsa2Scripts/estThickC"
inDir = homDir + relDir + "/py/dtsa2"
outDir = homDir + relDir + "/dat/csv"
jmg.ensureDir(outDir)
rptDir = inDir + '/simCarbonOnSi Results/'
def anaConSi(spc, det, digits=2, display=False):
"""anaConSi
Strip continuum and analyze a spectrum for C, on CuL
Parameters
----------
spc: A DTSA-II scriptable spectrum
The spectrum to process
det: The detector
vmrlEl = 50
przDepUm = 1.0
imgSzUm = 1.0
imgSize = 512 # pix
dose = 5000 # nA-sec
nDigits = 6
# directories
gitDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/utility"
prjDir = gitDir + relPrj
resDir = prjDir + '/sim-raft-on-zno-on-si'
jmg.ensureDir(resDir)
rptDir = prjDir + '/sim-raft-on-zno-on-si Results/'
spcDir = gitDir + '/dtsa2Scripts/spc/sim-raft-on-zno-on-si'
jmg.ensureDir(spcDir)
DataManager.clearSpectrumList()
start = time.time()
# define materials
zno = material("ZnO", density=5.61)
si = material("Si", density=2.33)
raft = material("C17H35O5S2P1", density=2.0)
raft.setName("RAFT polymer")
# specify the x-ray transitions
import time
import java.util as jutil
import java.io as jio
import java.nio.charset as cs
import string
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts"
prjDir = gitHom + relPrj
wrkDir = prjDir + "/mc3Scripts"
csvDir = wrkDir + "/dat/csv"
jmg.ensureDir(wrkDir)
os.chdir(wrkDir)
rptDir = wrkDir + '/simulateCoatedEagleXG Results/'
spcDir = wrkDir + "/dat/spc"
simDir = wrkDir + "/dat/sim"
jmg.ensureDir(spcDir)
jmg.ensureDir(simDir)
jmg.ensureDir(spcDir)
print(simDir)
det = findDetector("Oxford p4 05eV 2K")
e0 = 7 # kV
out = {
"C": (round(cInt[0] / dose, digits), round(cInt[1] / dose, digits)),
"Si": (round(siInt[0] / dose, digits), round(siInt[1] / dose, digits))
}
return out
start = time.time()
gitHom = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/mc3Scripts"
prjDir = gitHom + relPrj
datDir = prjDir + "/dat"
csvDir = datDir + "/csv"
jmg.ensureDir(datDir)
jmg.ensureDir(csvDir)
os.chdir(prjDir)
rptDir = prjDir + '/simulate-C-on-Si Results/'
det = findDetector("Oxford p4 05eV 2K")
e0 = 5 # kV
nTraj = 10000 # trajectories
lt = 100 # sec
pc = 0.25 # nA
tNmStepC = 10
tNmCMax = 100
dose = pc * lt # na-sec"
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 4K")
e0 = 15 # kV
nTraj = 10000 # trajectories
lt = 500 # sec
pc = 5.0 # nA
dose = pc * lt # na-sec"
bSaveSpc = True
gitHomeDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/sim-K309-quant/"
datDir = gitHomeDir + relPrj
print(gitHomeDir)
print(datDir)
"""
relPrj = "/Documents/work/dtsa2/sim-C-on-Si-7kV"
datDir = homDir + relPrj + "/msa-%g" % (nTraj)
jmg.ensureDir(datDir)
rptDir = homDir + relPrj + "/sim-C-on-Si-7kV Results"
csvFil = homDir + relPrj + "/dtsa2-C-on-Si-%g-kV-kratios-%g-traj.csv" % (e0, nTraj)
"""
start = time.time()
DataManager.clearSpectrumList()
"""
From N. Ritchie 2019-12-16
K309
Density 3 g/cm³
e0 = 20 # keV
pc = 2.5 # nA
lt = 100.0 # sec
imgSzUm = 5.0 # physical size of images in mucrons
imgSizePx = 512 # size of images in pixels
nTraj = 1000 # number of trajectories
vmrlEl = 40 # number of el for VMRL
dose = pc * lt # nA sec
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 + "/mc3SphereOnSubstrate Results"
al2o3 = epq.Material(
epq.Composition([epq.Element.Al, epq.Element.O], [0.5293, 0.4707]),
epq.ToSI.gPerCC(3.95))
al2o3.setName("Al2O3")
c = epq.Material(epq.Composition([epq.Element.C], [1.0]),
epq.ToSI.gPerCC(2.62))
c.setName("C")
xrts = [transition("Al K-L3"), transition("O K-L3"), transition("C K-L3")]
import dtsa2.mcSimulate3 as mc3
import dtsa2.jmGen as jmg
import dtsa2.jmMC3 as jm3
det = findDetector("Oxford p4 05eV 4K")
e0 = 15 # kV
nTraj = 10000 # trajectories
lt = 500 # sec
pc = 5.0 # nA
dose = pc * lt # na-sec"
bSaveSpc = True
gitHomeDir = os.environ['GIT_HOME']
relPrj = "/dtsa2Scripts/sim-srm_1155/"
datDir = gitHomeDir + relPrj
jmg.ensureDir(datDir)
print(gitHomeDir)
print(datDir)
srm1555_path = datDir + "sim-srm_1155.msa"
"""
relPrj = "/Documents/work/dtsa2/sim-C-on-Si-7kV"
datDir = homDir + relPrj + "/msa-%g" % (nTraj)
jmg.ensureDir(datDir)
rptDir = homDir + relPrj + "/sim-C-on-Si-7kV Results"
csvFil = homDir + relPrj + "/dtsa2-C-on-Si-%g-kV-kratios-%g-traj.csv" % (e0, nTraj)
"""
start = time.time()
now = datetime.now()
date_time = now.strftime("%m/%d/%Y, %H:%M:%S")
xtraParams.update(mc3.configureXRayAccumulators(xrts, True, True, True))
sim = mc3.multiFilm(layers,
det,
e0,
withPoisson=True,
nTraj=nTraj,
dose=dose,
sf=True,
bf=True,
xtraParams=xtraParams)
sName = "%g-nm-amC-on-%s-%g-kV" % (tc, mat, e0)
sim.rename(sName)
sim.getProperties().setTextProperty(epq.SpectrumProperties.SpectrumComment,
amcThickComment)
return sim
start = time.time()
projDir = homDir + "\\OneDrive\\Documents\\git\\dtsa2scripts\\sim-Pyrex\\"
print(projDir)
jmg.ensureDir(projDir)
spc = sim_amc_coated_mat(std, det, e0, nTraj, lt=100, pc=1.0, tc=20.0)
display(spc)
# rptDir = homDir + relPrj + "/sim-C-on-Si-7kV Results"
# csvFil = homDir + relPrj + "/dtsa2-C-on-Si-%g-kV-kratios-%g-traj.csv" % (e0, nTraj)
###
import glob import math import shutil import time import java.io as jio import dtsa2.jmGen as jmg edsDir = os.environ['EDS_ROOT'] relDir = "/Oxford/QM14-04-05A-Bauer" wd = edsDir + relDir + "/reports/py" os.chdir(wd) pyrDir="./anaSiBeamCal Results" datDir = edsDir + relDir + "/reports" spcDir = datDir + "/Si-pt6-5eV-2K" rptDir = datDir + "/csv" jmg.ensureDir(rptDir) rptFil = rptDir + "/probeCurrent.csv" sDet = "Oxford p6 05eV 2K" det = findDetector(sDet) wrkDist = 5.0 # mm spcBas = datDir + "/msa" jmg.ensureDir(spcBas) lNames = ["Si-7kV-Beam-Calib"] lPc = [] iCnt = 0
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)
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={}
import java.nio.charset as cs
import string
start = time.time()
homDir = os.environ['HOME']
homDir = homDir.replace('\\','/')
rPrjDir = "/Documents/git/dtsa2Scripts"
relIn = rPrjDir + "/utility"
relOut = rPrjDir + "/sim-Eagle-XG"
inDir = homDir + relIn
outDir = homDir + relOut
jmg.ensureDir(outDir)
rptDir = inDir + '/sim-C-ctd-CorningEagleXG-15kV Results/'
spcDir = outDir + "/sim"
simDir = outDir + "/sim"
jmg.ensureDir(spcDir)
jmg.ensureDir(simDir)
bVerbose = False
det = findDetector("Oxford p4 05eV 4K")
e0 = 15.0 # kV
nTraj = 20000 # trajectories
lt = 100 # sec
pc = 5.0 # nA
imgSize = 512 # pixel size for images
