def findLnLike(floats, datas):
""" SciPy Minimizer.
This could be moved to waveModel.py IF you decide you
don't need to look at the trace arrays anymore. """
global stTrace, enTrace, sloTrace
# Yeezus. At this point should you just write a damn class?
# Unpack parameters.
dataList, tempList, InterpFn = datas
data, dataTS, dataE, dataST, loWin, hiWin, dataNoise = dataList
temp, tempTS, tempE, tempST = tempList
st = en = slo = 0
if len(floats) == 1: # basinhopping case
slo, st, en = floats[0], dataST, dataE
if len(floats) == 3: # minimize case
st, en, slo = floats
# Make a trace
stTrace = np.append(stTrace, st)
enTrace = np.append(enTrace, en)
sloTrace = np.append(sloTrace, slo)
# print st, en, slo
# Build the model to compare with data
model, modelTS = wm.MakeModel(dataList,
tempList, [st, en, slo],
fn=InterpFn)
# Find LL and return
lnLike = 0.5 * np.sum(
np.power((data - model) / dataNoise, 2) -
np.log(1 / np.power(dataNoise, 2)))
return lnLike
def findLnLike(floats, datas):
""" SciPy Minimizer.
This could be moved to waveModel.py IF you decide you
don't need to look at the trace arrays anymore.
Also, the version in this file (match-minimizer.py)
is different because it tries to align the MAX time
(not the start time) of the waveforms.
"""
global mtTrace, enTrace, sloTrace
# Unpack parameters.
dataList, tempList, InterpFn = datas
data, dataTS, dataE, dataMax, loWin, hiWin, dataNoise = dataList
temp, tempTS, tempE, tempMax = tempList
# Can fix parameters here by setting them back to their input guess values
mt, en, slo = 0, 0, 0
if len(floats)==1: # basinhopping case
slo, mt, en = floats[0], dataMax, dataE
if len(floats)==3: # minimize case (no fixing)
mt, en, slo = floats
# Make a trace
mtTrace = np.append(mtTrace,mt)
enTrace = np.append(enTrace,en)
sloTrace = np.append(sloTrace,slo)
# print mt, en, slo
# Build the model to compare with data
model, modelTS = wm.MakeModel(dataList, tempList, [mt,en,slo], fn=InterpFn)
# Find LL of data vs. model
lnLike = 0.5 * np.sum ( np.power((data-model)/dataNoise, 2) - np.log( 1 / np.power(dataNoise,2) ) )
return lnLike
def findLnLike(floats, datas):
global stTrace, enTrace, sloTrace
# Unpack all parameters
st, en, slo = floats
dataList, tempList, InterpFn = datas
data, dataTS, dataE, dataST, loWin, hiWin, dataNoise = dataList
temp, tempTS, tempE, tempST = tempList
# Make a trace
stTrace = np.append(stTrace, st)
enTrace = np.append(enTrace, en)
sloTrace = np.append(sloTrace, slo)
# Build the model to compare with data
model, modelTS = wm.MakeModel(dataList, tempList, floats, fn=InterpFn)
# Return NLL
lnLike = -0.5 * np.sum(
np.power((data - model) / dataNoise, 2) -
np.log(1 / np.power(dataNoise, 2)))
return -1.0 * lnLike
def main():
""" Get a cool SciPy minimizer working and compare to MCMC. """
# Load data and template
npzfile = np.load("./data/optimumInputs.npz")
rl, tl = npzfile['arr_0'], npzfile['arr_1']
wave, waveTS, dataE, dataST = rl[0], rl[1], rl[2], rl[3]
temp, tempTS, tempE, tempST = tl[0], tl[1], tl[2], tl[3]
# Window the fit around rising edge - start time calculator method
loWin, hiWin = dataST - 1000, dataST + 4000 # ns
if loWin < waveTS[0] or hiWin > waveTS[-1]:
print "Window out of range! dataST: %.1f loWin %.1f hiWin %.1f" % (
dataST, loWin, hiWin)
idx = np.where((waveTS >= loWin) & (waveTS <= hiWin))
data = wave[idx]
dataTS = waveTS[idx]
# Pack into lists
dataNoise = 2. # just a guess - 1 sigma baseline adc values
rawList = [wave, waveTS, dataE, dataST]
dataList = [data, dataTS, dataE, dataST, loWin, hiWin, dataNoise]
tempList = [temp, tempTS, tempE, tempST]
# Recreate the guess and the guess's rising edge
guessFull, guessFullTS = wm.MakeModel(rawList,
tempList, [dataST, dataE, 1.],
opt="full")
guess, guessTS = wm.MakeModel(dataList,
tempList, [dataST, dataE, 1.],
opt="!fancy")
# Make an "almost complete" guess - no MCMC
# st, en, slo = dataST-100, dataE, 5
# InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
# model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Fit with MCMC and get best-fit parameters
numSteps, burnIn = 3000, 1800 # default: 10000, 5000. fast: 3000, 1800 long test: 20000,10000
wfModel = wm.TemplateModel(dataList, dataNoise, tempList)
M = pymc.MCMC(pymc.Model(wfModel))
M.use_step_method(pymc.Metropolis,
M.startTime,
proposal_sd=100.,
proposal_distribution='Normal')
M.use_step_method(pymc.Metropolis,
M.energy,
proposal_sd=1.,
proposal_distribution='Normal')
M.use_step_method(pymc.Metropolis,
M.slowness,
proposal_sd=100.,
proposal_distribution='Normal')
M.sample(iter=numSteps, verbose=0)
st = np.median(M.trace("startTime")[:])
en = np.median(M.trace("energy")[:])
slo = np.median(M.trace("slowness")[:])
InterpFn = interpolate.interp1d(tempTS,
temp,
kind="linear",
copy="False",
assume_sorted="True")
model, modelTS = wm.MakeModel(dataList,
tempList, [st, en, slo],
fn=InterpFn)
print "MCMC:", st, en, slo
# Fit with SciPy minimizer
MakeTracesGlobal(
) # creates 3 global arrays: startTrace, enTrace, sloTrace
floats = [dataST, dataE, 1]
print "Minimizer guesses:", floats
datas = [dataList, tempList, InterpFn]
result = minimize(findLnLike, floats, args=datas, method="Nelder-Mead")
st, en, slo = result["x"]
print "Minimizer: %.1f %.1f %.1f Success: %s. %s" % (
st, en, slo, result["success"], result["message"])
minimizer, minimizerTS = wm.MakeModel(dataList,
tempList, [st, en, slo],
fn=InterpFn)
# plots
fig = plt.figure(figsize=(11, 7), facecolor='w')
p1 = plt.subplot2grid((6, 7), (0, 0), colspan=4, rowspan=2) # original
p2 = plt.subplot2grid((6, 7), (2, 0), colspan=4, rowspan=3) # rising edge
p3 = plt.subplot2grid((6, 7), (0, 4), colspan=3, rowspan=2) # trace 1
p4 = plt.subplot2grid((6, 7), (2, 4), colspan=3, rowspan=2,
sharex=p3) # trace 2
p5 = plt.subplot2grid((6, 7), (4, 4), colspan=3, rowspan=2,
sharex=p3) # trace 3
# p1 = plt.subplot(211)
p1.set_title("Energy %.1f keV Start Time %.0f ns" % (dataE, dataST))
p1.set_ylabel("ADC [A.U.]", y=0.95, ha='right')
p1.set_xlabel("Time (ns)", x=0.95, ha='right')
p1.plot(waveTS, wave, color='blue', alpha=0.8, label='Data WF')
p1.plot(guessFullTS,
guessFull,
color='orange',
alpha=0.8,
label='Guess WF')
p1.axvline(x=dataST, color='green')
p1.legend(loc=4)
# p2 = plt.subplot(212)
p2.plot(dataTS, data, color='blue', label='Data')
p2.plot(guessTS, guess, color='orange', label='Guess')
p2.plot(modelTS, model, color='red', linewidth=4, alpha=0.8, label='MCMC')
p2.plot(minimizerTS,
minimizer,
color='cyan',
linewidth=1,
label='Nelder-Mead')
p2.legend(loc=4)
p3.cla()
p3.set_title("startTime %.1f Energy %.2f Slow %.1f" % (st, en, slo))
p3.plot(stTrace[1:])
p3.set_ylabel('startTime')
p4.cla()
p4.plot(enTrace[1:])
p4.set_ylabel('energy')
p5.cla()
p5.plot(sloTrace[1:])
p5.set_ylabel('slowness')
plt.tight_layout()
plt.subplots_adjust(hspace=0.35)
# plt.show(block=False)
# plt.show()
plt.savefig("./plots/minimizer-test.pdf")
def main():
# Load a data and a temp waveform
npzfile = np.load("./data/tailSlopeInputs.npz")
dl, tl = npzfile['arr_0'], npzfile['arr_1']
data, dataTS, dataE, dataRT = dl[0], dl[1], dl[2], dl[3]
temp, tempTS, tempE, tempRT = tl[0], tl[1], tl[2], tl[3]
print len(dataTS)
# Denoise, just for fun
wp = pywt.WaveletPacket(data=data,
wavelet='haar',
mode='symmetric',
maxlevel=3)
new_wp = pywt.WaveletPacket(data=None, wavelet='haar', mode='symmetric')
new_wp['aaa'] = wp['aaa'].data
waveDenoised = new_wp.reconstruct(update=False)
# ix = len(newWave)
# waveDenoised = np.delete(newWave, [ix-1,ix-2,ix-3])
# Start the tail slope fit ranged based on the calculated start time
# Plot the template "guess" to illustrate what we would expect to see
guessFull, guessFullTS = wm.MakeModel(dl,
tl, [dataRT, dataE, 1.],
opt="full")
idxMax = np.where(guessFull == guessFull.max()) # returns an array/tuple
idxMax = idxMax[0][0] # "cast" to int
idxMax += 100 # move it ahead in case this is a slow pulse
tail, tailTS = data[idxMax:], dataTS[idxMax:]
# Exponential fit
a, b = dataE, 72000
popt, pcov = curve_fit(wl.tailModelExp, tailTS, tail, p0=[a, b])
a, b = popt[0], popt[1]
# Polynomial curve fit
popt2, pcov2 = curve_fit(wl.tailModelPol, tailTS, tail)
d, e, f, g = popt2[0], popt2[1], popt2[2], popt2[3]
# Plots
fig = plt.figure(figsize=(8, 5), facecolor='w')
a1 = plt.subplot(111)
a1.set_ylabel("ADC", y=0.95, ha='right')
a1.set_xlabel("Time (ns)", x=0.95, ha='right')
a1.set_title("Energy %.1f StartTime %.1f %.1e * exp(-t/%.0f[us]) " %
(dataE, dataRT, a, b / 1000))
a1.plot(dataTS, data, color='blue', alpha=0.7, label='Data')
a1.plot(dataTS,
waveDenoised,
color='red',
alpha=0.8,
label='Lvl3 Haar Denoised')
a1.axvline(x=guessFullTS[np.where(guessFull == guessFull.max())],
color='black',
label='Guess Max ADC')
a1.plot(guessFullTS, guessFull, color='orange', label='Scaled Template WF')
a1.plot(tailTS,
wl.tailModelExp(tailTS, *popt),
color='cyan',
linewidth=2,
label='Tail Exp. Fit')
a1.plot(tailTS,
wl.tailModelPol(tailTS, *popt2),
color='green',
linewidth=2,
label='Tail Curve Fit')
a1.legend(loc=4)
plt.show()
def main(argv):
""" Interactive-fit or 'rapid'-fit waveforms that pass a given TCut.
BUG: Doesn't always work with a TChain. Add input files together
with hadd and use a single TFile.
"""
scanSpeed = 0.2
iList = -1
opt1 = ""
intMode, batMode = False, False
if (len(argv) >= 1): opt1 = argv[0]
if "-i" in (opt1):
intMode = True
print "Interactive mode selected."
if "-b" in (opt1):
batMode = True
print "Batch mode selected. A new file will be created."
# Load template waveform (created by gen-template.py)
npzfile = np.load("./data/genTemplateWF.npz")
temp, tempTS, tempE, tempST = npzfile['arr_0'] + 1, npzfile[
'arr_1'], npzfile['arr_2'], npzfile['arr_3'] * 10
# Set cuts
# theCut = inputFile.Get("cutUsedHere").GetTitle()
# DS3 "big DC" cut - PRELIMINARY
theCut = "trapENFCal > 0.8 && gain==0 && mHClean==1 && isGood && !muVeto && !wfDCBits && !isLNFill1 && !isLNFill2 && trapETailMin < 0 && channel!=596 && channel!=676 && channel!=676 && channel!=612 && channel!=1104 && channel!=1200 && channel!=1334 && channel!=1336 && tOffset < 10 && waveS5/TMath::Power(trapENFCal,1/4) < 1200 && (waveS3-waveS2)/trapENFCal > 100 && (waveS3-waveS2)/trapENFCal < 300 && !(channel==692 && (run==16974 || run==16975 || run==16976 || run==16977 || run==16978 || run==16979)) && butterTime < 11000"
# theCut += " && trapENFCal > 1.5 && trapENFCal < 2.1"
# theCut += " && trapENFCal < 20 && trapENFCal > 2 && run > 17480"
# theCut += " && kvorrT/trapENFCal > 2.2 && trapENFCal > 2 && trapENFCal < 10"
# Set file I/O and create entry lists
startT = time.clock()
inFile = "~/project/wavelet-skim/waveletSkimDS3_1.root"
# inFile = "~/project/wavelet-skim/hadd/waveletSkimDS3.root"
outFile = "~/project/fit-skim/fitSkimDS3_1.root"
inputFile = TFile(inFile)
waveTree = inputFile.Get("skimTree")
print "Found", waveTree.GetEntries(
), "input entries. Using cut:\n", theCut, "\n"
waveTree.Draw(">>elist", theCut, "entrylist")
elist = gDirectory.Get("elist")
waveTree.SetEntryList(elist)
nList = elist.GetN()
print "Found", nList, "entries passing cuts."
stopT = time.clock()
print "Data loading time (s): ", (stopT - startT)
# In batch mode ONLY, create an output file+tree & append new branches
outputFile = TFile()
outTree = TTree()
if batMode:
outputFile = TFile(outFile, "RECREATE")
print "Attempting tree copy to", outFile
outTree = waveTree.CopyTree("")
outTree.Write()
print "Wrote", outTree.GetEntries(), "entries."
cutUsed = TNamed("cutUsedHere", theCut)
cutUsed.Write()
fitStart = std.vector("double")()
fitE = std.vector("double")()
fitSlo = std.vector("double")()
fitStartSD = std.vector("double")()
fitESD = std.vector("double")()
fitSloSD = std.vector("double")()
fitChi2NDF = std.vector("double")()
fitLnLike = std.vector("double")()
tExp1 = std.vector("double")()
tExp2 = std.vector("double")()
tPol0 = std.vector("double")()
tPol1 = std.vector("double")()
tPol2 = std.vector("double")()
tPol3 = std.vector("double")()
baseAvg = std.vector("double")()
baseNoise = std.vector("double")()
bFitStart = outTree.Branch("fitStart", fitStart)
bFitE = outTree.Branch("fitE", fitE)
bFitSlo = outTree.Branch("fitSlo", fitSlo)
bFitStart_sd = outTree.Branch("fitStartSD", fitStartSD)
bFitE_sd = outTree.Branch("fitESD", fitESD)
bFitSlo_sd = outTree.Branch("fitSloSD", fitSloSD)
bFitChi2NDF = outTree.Branch("fitChi2NDF", fitChi2NDF)
bFitLnLike = outTree.Branch("fitLnLike", fitLnLike)
bTExp1 = outTree.Branch("tExp1", tExp1)
bTExp2 = outTree.Branch("tExp2", tExp2)
bTPol0 = outTree.Branch("tPol0", tPol0)
bTPol1 = outTree.Branch("tPol1", tPol1)
bTPol2 = outTree.Branch("tPol2", tPol2)
bTPol3 = outTree.Branch("tPol3", tPol3)
bBaseAvg = outTree.Branch("baseAvg", baseAvg)
bBaseNoise = outTree.Branch("baseNoise", baseNoise)
# Make a figure
# with PdfPages('multipage_pdf.pdf') as pdf:
fig = plt.figure(figsize=(11, 7), facecolor='w')
p1 = plt.subplot2grid((6, 7), (0, 0), colspan=4, rowspan=2) # original
p2 = plt.subplot2grid((6, 7), (2, 0), colspan=4, rowspan=3) # rising edge
p3 = plt.subplot2grid((6, 7), (5, 0), colspan=4, rowspan=1) # residual
p4 = plt.subplot2grid((6, 7), (0, 4), colspan=3, rowspan=2) # trace 1
p5 = plt.subplot2grid((6, 7), (2, 4), colspan=3, rowspan=2,
sharex=p4) # trace 2
p6 = plt.subplot2grid((6, 7), (4, 4), colspan=3, rowspan=2,
sharex=p4) # trace 3
if not batMode: plt.show(block=False)
# Setup multiprocessing
manager = Manager()
returnDict = manager.dict()
# Loop over events
while (True):
saveMe = False
iList += 1
if intMode == True and iList != 0:
value = raw_input()
if value == 'q': break
if value == 's': saveMe = True
if value == 'p': iList -= 2 # previous
if (value.isdigit()): iList = int(value) # go to entry
if iList >= elist.GetN(): break
entry = waveTree.GetEntryNumber(iList)
waveTree.LoadTree(entry)
waveTree.GetEntry(entry)
nChans = waveTree.channel.size()
numPass = waveTree.Draw("channel", theCut, "GOFF", 1, iList)
chans = waveTree.GetV1()
chanList = list(set(int(chans[n]) for n in xrange(numPass)))
fitStart.assign(nChans, -9999)
fitE.assign(nChans, -9999)
fitSlo.assign(nChans, -9999)
fitStartSD.assign(nChans, -9999)
fitESD.assign(nChans, -9999)
fitSloSD.assign(nChans, -9999)
fitChi2NDF.assign(nChans, -9999)
fitLnLike.assign(nChans, -9999)
tExp1.assign(nChans, -9999)
tExp2.assign(nChans, -9999)
tPol0.assign(nChans, -9999)
tPol1.assign(nChans, -9999)
tPol2.assign(nChans, -9999)
tPol3.assign(nChans, -9999)
baseAvg.assign(nChans, -9999)
baseNoise.assign(nChans, -9999)
# Loop over hits passing cuts
hitList = (iH for iH in xrange(nChans)
if waveTree.channel.at(iH) in chanList
) # a 'generator expression'
for iH in hitList:
# Load waveform for this hit
run = waveTree.run
chan = waveTree.channel.at(iH)
dataE = waveTree.trapENFCal.at(iH)
dataST = waveTree.butterTime.at(iH) # replace with blrwfFMR50?
toe = waveTree.kvorrT.at(iH) / dataE
print "%d / %d Run %d nCh %d chan %d trapENF %.1f t/e %.1f" % (
iList, nList, run, nChans, chan, dataE, toe)
signal = wl.processWaveform(waveTree.MGTWaveforms.at(iH),
opt='full')
waveBLSub = signal.GetWaveBLSub()
waveFilt = signal.GetWaveFilt()
waveTS = signal.GetTS()
dataBaseline, dataNoise = signal.GetBaseNoise()
# Denoise the data waveform (take only lowest-frequency components)
wp = pywt.WaveletPacket(data=waveBLSub,
wavelet='haar',
mode='symmetric',
maxlevel=3)
new_wp = pywt.WaveletPacket(data=None,
wavelet='haar',
mode='symmetric')
new_wp['aaa'] = wp['aaa'].data
waveDenoised = new_wp.reconstruct(update=False)
# Window the fit around rising edge - start time calculator method
loWin, hiWin = dataST - 1000, dataST + 4000 # ns
if loWin < waveTS[0] or hiWin > waveTS[-1]:
print "Window out of range! dataST: %.1f loWin %.1f hiWin %.1f" % (
dataST, loWin, hiWin)
idx = np.where((waveTS >= loWin) & (waveTS <= hiWin))
data = waveBLSub[idx]
# data = waveDenoised[idx]
dataTS = waveTS[idx]
# Pack into lists
rawList = [waveBLSub, waveTS, dataE, dataST]
dataList = [data, dataTS, dataE, dataST, loWin, hiWin]
tempList = [temp, tempTS, tempE, tempST]
# Optionally save something to a file
if saveMe:
print "Saved entry", iList, iH
np.savez("./data/tailSlopeInputs.npz", rawList, tempList)
# Recreate the guess and the guess's rising edge
guessFull, guessFullTS = wm.MakeModel(dataList,
tempList,
[dataST, dataE, 1.],
opt="full")
guess, guessTS = wm.MakeModel(dataList,
tempList, [dataST, dataE, 1.],
opt="!fancy")
# Make an "almost complete" guess - no MCMC
# st, en, slo = dataST-100, dataE, 5
# InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
# model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Fit with MCMC and get best-fit parameters
numSteps, burnIn = 3000, 1800 # default: 10000, 5000. fast: 3000, 1800 long test: 20000,10000
wfModel = wm.TemplateModel(dataList, dataNoise, tempList)
p = Process(target=RunMCMC,
args=(wfModel, numSteps, burnIn, returnDict))
p.start()
p.join()
startTimeTr = returnDict["startTimeTr"]
energyTr = returnDict["energyTr"]
slownessTr = returnDict["slownessTr"]
st = np.median(startTimeTr[burnIn:])
en = np.median(energyTr[burnIn:])
slo = np.median(slownessTr[burnIn:])
InterpFn = interpolate.interp1d(tempTS,
temp,
kind="linear",
copy="False",
assume_sorted="True")
model, modelTS = wm.MakeModel(dataList,
tempList, [st, en, slo],
fn=InterpFn)
# Save some extra parameters for the ROOT output
# Calculate residual, Chi2/NDF, likelihood, etc.
st_std = np.std(startTimeTr[burnIn:])
en_std = np.std(energyTr[burnIn:])
slo_std = np.std(slownessTr[burnIn:])
residual = model - data
frac = (np.power(data - model, 2)) / np.abs(model)
chi2NDF = np.sum(frac) / len(model)
inv_sigma2 = 1.0 / (dataNoise**2)
lnLike = -0.5 * (np.sum((data - model)**2 * inv_sigma2 -
np.log(inv_sigma2)))
# ** Do a separate & simple fit of the tail slope **
# TODO: Add this to process-waveforms.py
idxMax = np.where(
guessFull == guessFull.max()) # returns an array/tuple
idxMax = idxMax[0][0] # "cast" to int
tail, tailTS = waveDenoised[idxMax:], waveTS[idxMax:]
popt, _ = curve_fit(wl.tailModelPol, tailTS, tail) # poly fit
pol0, pol1, pol2, pol3 = popt[0], popt[1], popt[2], popt[3]
a, b = dataE, 72000
popt2, _ = curve_fit(wl.tailModelExp, tailTS, tail,
p0=[a, b]) # expo fit
e1, e2 = popt2[0], popt2[1]
# Assign values to output vectors and fill branches
fitStart[iH], fitStartSD[iH] = st, st_std
fitE[iH], fitESD[iH] = en, en_std
fitSlo[iH], fitSloSD[iH] = slo, slo_std
fitChi2NDF[iH] = chi2NDF
fitLnLike[iH] = lnLike
tExp1[iH], tExp2[iH] = e1, e2
tPol0[iH], tPol1[iH], tPol2[iH], tPol3[iH] = pol0, pol1, pol2, pol3
baseAvg[iH] = dataBaseline
baseNoise[iH] = dataNoise
if batMode:
bFitStart.Fill()
bFitE.Fill()
bFitSlo.Fill()
bFitStart_sd.Fill()
bFitE_sd.Fill()
bFitSlo_sd.Fill()
bFitChi2NDF.Fill()
bFitLnLike.Fill()
bTExp1.Fill()
bTExp2.Fill()
bTPol0.Fill()
bTPol1.Fill()
bTPol2.Fill()
bTPol3.Fill()
bBaseAvg.Fill()
bBaseNoise.Fill()
if iList % 5000 == 0:
outTree.Write("", TObject.kOverwrite)
print "%d / %d entries saved (%.2f %% done)." % (
iList, nList, 100 * (float(iList) / nList))
# If not in batch mode, fill the figure
if batMode: continue
p1.cla()
p1.set_ylabel("ADC")
p1.set_title(
"Run %d Channel %d Entry %d\ntrapENFCal %.1f T/E %.1f ST %.1f"
% (run, chan, iList, dataE, toe, dataST))
p1.plot(waveTS, waveBLSub, color='blue')
p1.plot(waveTS, waveDenoised, color='red', alpha=0.8)
p1.plot(guessFullTS, guessFull, color='orange', linewidth=2)
p1.axvline(x=dataST, color='green', linewidth=2)
p1.axvline(x=loWin, color='black')
p1.axvline(x=hiWin, color='black')
p1.plot(tailTS,
wl.tailModelPol(tailTS, *popt),
color='cyan',
linewidth=1) # tail poly fit
p1.plot(tailTS,
wl.tailModelExp(tailTS, *popt2),
color='cyan',
linewidth=1) # tail expo fit
p2.cla()
p2.plot(dataTS, data, color='blue', label='Data')
p2.plot(guessTS, guess, color='orange', label='Guess')
# special: plot the values of the trace after burn-in
# to see how the model is covering the "money-zone"/rising edge after it's converged.
# for i in range(burnIn,numSteps):
# st_tr, en_tr, slo_tr = M.trace('startTime')[i], M.trace('energy')[i], M.trace('slowness')[i]
# trace, traceTS = wm.MakeModel(dataList, tempList, [st_tr,en_tr,slo_tr], fn=InterpFn)
# p2.plot(traceTS, trace, color='red',alpha=0.1,linewidth=2)
p2.plot(modelTS,
model,
color='red',
linewidth=3,
alpha=0.7,
label='Best Fit')
p2.legend(loc=4)
p3.cla()
p3.set_xlabel("Time [ns]", x=0.95, ha='right')
p3.set_ylabel("Residual [ADC]")
p3.plot(modelTS, residual, color='red')
p3.axhline(y=0, color='blue', alpha=0.3)
p3.axhline(y=dataNoise, color='blue', alpha=0.3)
p3.axhline(y=-1.0 * dataNoise, color='blue', alpha=0.3)
p4.cla()
minST = tempST - tempTS[-1] + hiWin
maxST = tempST - tempTS[0] + loWin
p4.set_title(
"startTime %.1f Energy %.2f\nSlow %.1f chi2/ndf %.1f Min %d Max %d"
% (st, en, slo, chi2NDF, minST, maxST))
p4.plot(startTimeTr[:])
p4.set_ylabel('startTime')
p4.axvline(x=burnIn, color='red', alpha=0.5)
p5.cla()
p5.plot(energyTr[:])
p5.set_ylabel('energy')
p5.axvline(x=burnIn, color='red', alpha=0.5)
p6.cla()
p6.plot(slownessTr[:])
p6.set_ylabel('slowness')
p6.axvline(x=burnIn, color='red', alpha=0.5)
plt.tight_layout()
plt.subplots_adjust(hspace=0.35)
plt.pause(scanSpeed)
# pdf.savefig()
# End loop over events
if batMode:
outTree.Write("", TObject.kOverwrite)
print "Wrote", outTree.GetBranch(
"channel").GetEntries(), "entries in the copied tree,"
print "and wrote", bFitStart.GetEntries(
), "entries in the new branches."
def main(argv):
""" Interactive-fit or 'rapid'-fit waveforms that pass a given TCut.
BUG: Doesn't always work with a TChain. Add input files together
with hadd and use a single TFile.
"""
scanSpeed = 1.
iList = -1
opt1 = ""
intMode = False
if (len(argv) >= 1): opt1 = argv[0]
if "-i" in (opt1): intMode = True
# Set input data and cuts
inputFile = TFile(
"~/project/match-skim/waveletSkimDS5_run23920.root") # calibration
# inputFile = TFile("~/project/v2-processwfs/waveletSkimDS5_90.root") # noisy BG
waveTree = inputFile.Get("skimTree")
theCut = inputFile.Get("cutUsedHere").GetTitle()
theCut += " && waveS5/trapENFCal < 1200 && trapENFCal > 1.5 && trapENFCal < 3"
# Print cut and events passing cut
waveTree.Draw(">>elist", theCut, "entrylist")
elist = gDirectory.Get("elist")
waveTree.SetEntryList(elist)
nList = elist.GetN()
print "Using cut:\n", theCut, "\n"
print "Found", waveTree.GetEntries(), "input entries."
print "Found", nList, "entries passing cuts."
# Make a figure
fig = plt.figure(figsize=(15, 10), facecolor='w')
p1 = plt.subplot2grid((6, 7), (0, 0), colspan=4, rowspan=2) # original
p2 = plt.subplot2grid((6, 7), (2, 0), colspan=4, rowspan=3) # rising edge
p3 = plt.subplot2grid((6, 7), (5, 0), colspan=4, rowspan=1) # residual
p4 = plt.subplot2grid((6, 7), (0, 4), colspan=3, rowspan=2) # trace 1
p5 = plt.subplot2grid((6, 7), (2, 4), colspan=3, rowspan=2) # trace 2
p6 = plt.subplot2grid((6, 7), (4, 4), colspan=3, rowspan=2) # trace 3
plt.show(block=False)
# Make template(s)
# npzfile = np.load("./data/genTemplateWF.npz") # gen-template.py
# temp, tempTS, tempE, tempST = npzfile['arr_0']+1, npzfile['arr_1'], npzfile['arr_2'], npzfile['arr_3']*10
samp, r, z, tempE, tempST, smooth = 2016, 0, 15, 3938, 1000, 100 # gen-template.py
# samp, r, z, tempE, tempST, smooth = 5000, 0, 15, 10, 2500, 100 # huge template
# samp, r, z, tempE, tempST, smooth = 2016, 0, 15, 10, 1000, 100 # regular size template
# samp, r, z, tempE, tempST, smooth = 2016, 30, 30, 10, 1000, 100 # regular size temp, slower rise
# samp, r, z, tempE, tempST, smooth = 500, 0, 15, 10, 100, 100 # small template
temp, tempTS = wl.MakeSiggenWaveform(samp, r, z, tempE, tempST, smooth)
tempST = tempST * 10 # convert to ns
# Loop over events
while True:
saveMe = False
iList += 1
if intMode == True and iList != 0:
value = raw_input()
if value == 'q': break
if value == 's': saveMe = True
if value == 'p': iList -= 2 # previous
if (value.isdigit()): iList = int(value) # go to entry
if iList >= elist.GetN(): break
entry = waveTree.GetEntryNumber(iList)
waveTree.LoadTree(entry)
waveTree.GetEntry(entry)
nChans = waveTree.channel.size()
numPass = waveTree.Draw("channel", theCut, "GOFF", 1, iList)
chans = waveTree.GetV1()
chanList = list(set(int(chans[n]) for n in xrange(numPass)))
# Loop over hits passing cuts
hitList = (iH for iH in xrange(nChans)
if waveTree.channel.at(iH) in chanList
) # a 'generator expression'
for iH in hitList:
# ------------------------------------------------------------------------
# Load waveform for this hit
run = waveTree.run
chan = waveTree.channel.at(iH)
dataE = waveTree.trapENFCal.at(iH)
dataST = waveTree.butterTime.at(iH) # replace with blrwfFMR50?
toe = waveTree.kvorrT.at(iH) / dataE
print "%d / %d Run %d nCh %d chan %d trapENF %.1f t/e %.1f" % (
iList, nList, run, nChans, chan, dataE, toe)
signal = wl.processWaveform(waveTree.MGTWaveforms.at(iH),
opt='full')
waveBLSub = signal.GetWaveBLSub()
waveFilt = signal.GetWaveFilt()
waveTS = signal.GetTS()
baseAvg, dataNoise = signal.GetBaseNoise()
# Denoise the data waveform (take only lowest-frequency components)
wp = pywt.WaveletPacket(data=waveBLSub,
wavelet='haar',
mode='symmetric',
maxlevel=3)
new_wp = pywt.WaveletPacket(data=None,
wavelet='haar',
mode='symmetric')
new_wp['aaa'] = wp['aaa'].data
waveDenoised = new_wp.reconstruct(update=False)
# Window the fit around rising edge - start time calculator method
loWin, hiWin = dataST - 1000, dataST + 4000 # ns
if loWin < waveTS[0] or hiWin > waveTS[-1]:
print "Window out of range! dataST: %.1f loWin %.1f hiWin %.1f" % (
dataST, loWin, hiWin)
idx = np.where((waveTS >= loWin) & (waveTS <= hiWin))
data = waveBLSub[idx]
# data = waveDenoised[idx]
dataTS = waveTS[idx]
# Pack into lists
rawList = [waveBLSub, waveTS, dataE, dataST]
dataList = [data, dataTS, dataE, dataST, loWin, hiWin, dataNoise]
tempList = [temp, tempTS, tempE, tempST]
# Optionally save something to a file
if saveMe:
np.savez("./data/tailSlopeInputs.npz", rawList, tempList)
# Recreate the guess and the guess's rising edge
guessFull, guessFullTS = wm.MakeModel(dataList,
tempList,
[dataST, dataE, 1.],
opt="full")
guess, guessTS = wm.MakeModel(dataList,
tempList, [dataST, dataE, 1.],
opt="!fancy")
# Make an "almost complete" guess - no fitting
# st, en, slo = dataST-100, dataE, 5
InterpFn = interpolate.interp1d(tempTS,
temp,
kind="linear",
copy="False",
assume_sorted="True")
# model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Fit with MCMC and get best-fit parameters
# numSteps, burnIn = 10000, 5000 # default - 10000, 5000. try 3000, 2000. long test: 20000,10000
# myModel = TemplateModel( dataList, dataNoise, tempList )
# waveModel = pymc.Model( myModel )
# M = pymc.MCMC( waveModel )
# M.use_step_method(pymc.Metropolis, M.startTime, proposal_sd=100., proposal_distribution='Normal')
# M.use_step_method(pymc.Metropolis, M.energy, proposal_sd=1., proposal_distribution='Normal')
# M.use_step_method(pymc.Metropolis, M.slowness, proposal_sd=100., proposal_distribution='Normal')
# M.sample(iter=numSteps, verbose=0) # do the fit
# st = np.median(M.trace('startTime')[burnIn:])
# en = np.median(M.trace('energy')[burnIn:])
# slo = np.median(M.trace('slowness')[burnIn:])
# InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
# model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Fit with SciPy minimizer(s) and get best-fit parameters
# how long does it take?
start = time.time()
MakeTracesGlobal(
) # creates 3 global arrays: startTrace, enTrace, sloTrace
datas = [dataList, tempList, InterpFn]
# floats = [1.]
# result = op.basinhopping(findLnLike, floats, T=1000, stepsize=15, niter_success=2, minimizer_kwargs={"args":datas})
# print "slowness:",result["x"],"dataE",dataE,"dataST",dataST
# floats = [dataST, dataE, result["x"]]
# MakeTracesGlobal() # resets traces
floats = [dataST, dataE, 20.]
result = op.minimize(findLnLike,
floats,
args=datas,
method="Nelder-Mead")
if not result["success"]: print result["message"]
st, en, slo = result["x"]
model, modelTS = wm.MakeModel(dataList,
tempList, [st, en, slo],
fn=InterpFn)
stop = time.time()
print "fitting took", stop - start
# Calculate residual, Chi2/NDF, likelihood, etc.
residual = model - data
frac = (np.power(data - model, 2)) / np.abs(model)
chi2NDF = np.sum(frac) / len(model)
inv_sigma2 = 1.0 / (dataNoise**2)
lnLike = -0.5 * (np.sum((data - model)**2 * inv_sigma2 -
np.log(inv_sigma2)))
# Fill the figure
p1.cla()
p1.set_ylabel("ADC")
p1.set_title(
"Run %d Channel %d Entry %d\ntrapENFCal %.1f T/E %.1f ST %.1f"
% (run, chan, iList, dataE, toe, dataST))
p1.plot(waveTS, waveBLSub, color='blue')
p1.plot(waveTS, waveDenoised, color='red', alpha=0.8)
p1.plot(guessFullTS, guessFull, color='orange', linewidth=2)
p1.axvline(x=dataST, color='green', linewidth=2)
p1.axvline(x=loWin, color='black')
p1.axvline(x=hiWin, color='black')
p2.cla()
p2.plot(dataTS, data, color='blue', label='Data')
p2.plot(guessTS, guess, color='orange', label='Guess')
p2.plot(modelTS, model, color='red', linewidth=3, label='Best Fit')
p2.legend(loc=4)
p3.cla()
p3.set_xlabel("Time [ns]", x=0.95, ha='right')
p3.set_ylabel("Residual [ADC]")
p3.plot(guessTS, residual, color='red')
p3.axhline(y=0, color='blue', alpha=0.3)
p3.axhline(y=dataNoise, color='blue', alpha=0.3)
p3.axhline(y=-1.0 * dataNoise, color='blue', alpha=0.3)
p4.cla()
p4.set_title("startTime %.1f Energy %.2f Slow %.1f" %
(st, en, slo))
p4.plot(stTrace[1:])
p4.set_ylabel('startTime')
p5.cla()
p5.plot(enTrace[1:])
p5.set_ylabel('energy')
p6.cla()
p6.plot(sloTrace[1:])
p6.set_ylabel('slowness')
plt.tight_layout()
plt.subplots_adjust(hspace=0.35)
plt.pause(scanSpeed)
def main(argv):
""" Interactive-fit or 'rapid'-fit waveforms that pass a given TCut.
BUG: Doesn't always work with a TChain. Add input files together
with hadd and use a single TFile.
"""
scanSpeed = 0.2
iList = -1
opt1, opt2 = "", "-"
intMode = False
if (len(argv) >= 1): opt1 = argv[0]
if (len(argv) >= 2): opt2 = argv[1]
if "-i" in (opt1, opt2):
intMode = True
print "Interactive mode selected."
startT = time.clock()
# Load template waveforms
templateFile = TFile("./data/wave-m1cal.root")
waveTemplates = templateFile.Get("waveTree")
calDict = {640:28, 672:18, 610:16, 580:19, 582:34, 648:38, 600:21, 578:39, 592:27, 664:55, 626:62, 692:8, 598:22, 690:52, 632:9, 608:7}
# PlotTemplateWaveforms(waveTemplates,calDict)
# return
# Set input data and cuts
inputFile = TFile("~/project/wavelet-skim/hadd/waveletSkimDS3.root")
# inputFile = TFile("~/project/wavelet-skim/waveletSkimDS3_13.root")
waveTree = inputFile.Get("skimTree")
print "Found",waveTree.GetEntries(),"input entries."
# theCut = inputFile.Get("cutUsedHere").GetTitle()
# DS3 big cut
theCut = "trapENFCal > 0.8 && gain==0 && mHClean==1 && isGood && !muVeto && !wfDCBits && !isLNFill1 && !isLNFill2 && trapETailMin < 0 && channel!=596 && channel!=676 && channel!=676 && channel!=612 && channel!=1104 && channel!=1200 && channel!=1334 && channel!=1336 && tOffset < 10 && waveS5/TMath::Power(trapENFCal,1/4) < 1200 && (waveS3-waveS2)/trapENFCal > 100 && (waveS3-waveS2)/trapENFCal < 300 && !(channel==692 && (run==16974 || run==16975 || run==16976 || run==16977 || run==16978 || run==16979)) && butterTime < 11000"
# theCut += " && trapENFCal > 2 && trapENFCal < 2.1 && channel==578 && run==16868" # template fast WF (2kev)
theCut += " && trapENFCal > 7 && trapENFCal < 10"
# theCut += " && trapENFCal < 20 && trapENFCal > 2 && run > 17480"
# theCut += " && kvorrT/trapENFCal > 2.2 && trapENFCal > 2 && trapENFCal < 10"
# Print cut and events passing cut
print "Using cut:\n",theCut,"\n"
waveTree.Draw(">>elist", theCut, "entrylist")
elist = gDirectory.Get("elist")
waveTree.SetEntryList(elist)
nList = elist.GetN()
print "Found",nList,"entries passing cuts."
stopT=time.clock()
print "Data loading time (s): ", (stopT-startT)
# Make a figure
fig = plt.figure(figsize=(11,7), facecolor='w')
p1 = plt.subplot2grid((6,7), (0,0), colspan=4, rowspan=2) # original
p2 = plt.subplot2grid((6,7), (2,0), colspan=4, rowspan=3) # rising edge
p3 = plt.subplot2grid((6,7), (5,0), colspan=4, rowspan=1) # residual
p4 = plt.subplot2grid((6,7), (0,4), colspan=3, rowspan=2 ) # trace 1
p5 = plt.subplot2grid((6,7), (2,4), colspan=3, rowspan=2, sharex=p4) # trace 2
p6 = plt.subplot2grid((6,7), (4,4), colspan=3, rowspan=2, sharex=p4) # trace 3
plt.show(block=False)
# Loop over events
while(True):
saveMe = False
iList += 1
if intMode==True and iList != 0:
value = raw_input()
if value=='q': break
if value=='s': saveMe=True
if value=='p': iList -= 2 # previous
if (value.isdigit()): iList = int(value) # go to entry
if iList >= elist.GetN(): break
entry = waveTree.GetEntryNumber(iList);
waveTree.LoadTree(entry)
waveTree.GetEntry(entry)
nChans = waveTree.channel.size()
numPass = waveTree.Draw("channel",theCut,"GOFF",1,iList)
chans = waveTree.GetV1()
chanList = list(set(int(chans[n]) for n in xrange(numPass)))
# Loop over hits passing cuts
hitList = (iH for iH in xrange(nChans) if waveTree.channel.at(iH) in chanList) # a 'generator expression'
for iH in hitList:
# Load waveform for this hit
run = waveTree.run
chan = waveTree.channel.at(iH)
dataE = waveTree.trapENFCal.at(iH)
dataST = waveTree.butterTime.at(iH) # replace with blrwfFMR50?
toe = waveTree.kvorrT.at(iH)/dataE
print "%d / %d Run %d nCh %d chan %d trapENF %.1f t/e %.1f" % (iList,nList,run,nChans,chan,dataE,toe)
signal = wl.processWaveform(waveTree.MGTWaveforms.at(iH),opt='full')
waveBLSub = signal.GetWaveBLSub()
waveFilt = signal.GetWaveFilt()
waveTS = signal.GetTS()
baseAvg, dataNoise = signal.GetBaseNoise()
# Denoise the data waveform (take only lowest-frequency components)
wp = pywt.WaveletPacket(data=waveBLSub, wavelet='haar', mode='symmetric',maxlevel=3)
new_wp = pywt.WaveletPacket(data=None, wavelet='haar', mode='symmetric')
new_wp['aaa'] = wp['aaa'].data
waveDenoised = new_wp.reconstruct(update=False)
# Load channel template waveform
try: tempEntry = calDict[chan]
except:
print "ain't got channel",chan
continue
waveTemplates.GetEntry(calDict[chan])
template = wl.processWaveform(waveTemplates.event.GetWaveform(waveTemplates.itr),opt='full')
temp = template.GetWaveBLSub()
tempTS = template.GetTS()
tempE = waveTemplates.trapENFCal
tempST = waveTemplates.blrwfFMR50
# Window the fit around rising edge - start time calculator method
loWin, hiWin = dataST - 1000, dataST + 4000 # ns
if loWin < waveTS[0] or hiWin > waveTS[-1]:
print "Window out of range! dataST: %.1f loWin %.1f hiWin %.1f" % (dataST,loWin,hiWin)
idx = np.where((waveTS >= loWin) & (waveTS <= hiWin))
data = waveBLSub[idx]
# data = waveDenoised[idx]
dataTS = waveTS[idx]
# Pack into lists
rawList = [waveBLSub, waveTS, dataE, dataST]
dataList = [data, dataTS, dataE, dataST, loWin, hiWin]
tempList = [temp, tempTS, tempE, tempST]
# Optionally save to a file
if saveMe:
print "Saved entry",iList,iH
np.savez("./data/optimumInputs.npz",rawList,tempList)
# np.savez("./data/rawInputs.npz",rawList)
# Recreate the guess and the guess's rising edge
guessFull, guessFullTS = wm.MakeModel(dataList, tempList, [dataST,dataE,1.], opt="full")
guess, guessTS = wm.MakeModel(dataList, tempList, [dataST,dataE,1.], opt="!fancy")
# Make an "almost complete" guess - no MCMC
# st, en, slo = dataST-100, dataE, 5
# InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
# model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Fit with MCMC and get best-fit parameters
numSteps, burnIn = 2000, 1000 # default - 10000, 5000. try 3000, 2000
myModel = wm.TemplateModel( dataList, dataNoise, tempList )
waveModel = pymc.Model( myModel )
M = pymc.MCMC( waveModel )
M.use_step_method(pymc.Metropolis, M.startTime, proposal_sd=100., proposal_distribution='Normal')
M.use_step_method(pymc.Metropolis, M.energy, proposal_sd=1., proposal_distribution='Normal')
M.use_step_method(pymc.Metropolis, M.slowness, proposal_sd=100., proposal_distribution='Normal')
M.sample(iter=numSteps, verbose=0) # do the fit
st = np.median(M.trace('startTime')[burnIn:])
en = np.median(M.trace('energy')[burnIn:])
slo = np.median(M.trace('slowness')[burnIn:])
InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
model, modelTS = wm.MakeModel(dataList, tempList, [st,en,slo], fn=InterpFn)
# Calculate residual, Chi2/NDF
residual = model - data
frac = (np.power(data - model, 2)) / np.abs(model)
chi2NDF = np.sum(frac) / len(model)
print "chi2/NDF:",chi2NDF
# ** Do a separate & simple fit of the tail slope **
# TODO: Add this to process-waveforms.py
idxMax = np.where(guessFull == guessFull.max()) # returns an array/tuple
idxMax = idxMax[0][0] # "cast" to int
tail, tailTS = waveDenoised[idxMax:], waveTS[idxMax:]
popt,_ = curve_fit(wl.tailModelPol, tailTS, tail) # poly fit
a, b = dataE, 72000
popt2,_ = curve_fit(wl.tailModelExp, tailTS, tail, p0=[a,b]) # expo fit
# Fill the figure
p1.cla()
p1.set_ylabel("ADC")
p1.set_title("Run %d Channel %d Entry %d\ntrapENFCal %.1f T/E %.1f ST %.1f" % (run,chan,iList,dataE,toe,dataST))
p1.plot(waveTS,waveBLSub,color='blue')
p1.plot(waveTS,waveDenoised,color='red',alpha=0.8)
p1.plot(guessFullTS,guessFull,color='orange',linewidth=2)
p1.axvline(x = dataST, color='green',linewidth=2)
p1.axvline(x = loWin, color='black')
p1.axvline(x = hiWin, color='black')
p1.plot(tailTS, wl.tailModelPol(tailTS, *popt), color='cyan', linewidth=1) # tail poly fit
p1.plot(tailTS, wl.tailModelExp(tailTS, *popt2), color='cyan', linewidth=1) # tail expo fit
p2.cla()
p2.plot(dataTS,data,color='blue',label='Data')
p2.plot(guessTS,guess,color='orange',label='Guess')
p2.plot(modelTS,model,color='red',linewidth=3,alpha=0.7,label='Fit')
p2.legend(loc=4)
p3.cla()
p3.set_xlabel("Time [ns]", x=0.95, ha='right')
p3.set_ylabel("Residual [ADC]")
p3.plot(modelTS,residual, color='red')
p3.axhline(y = 0, color='blue', alpha=0.3)
p3.axhline(y = dataNoise, color='blue', alpha=0.3)
p3.axhline(y = -1.0*dataNoise, color='blue', alpha=0.3)
p4.cla()
minST = tempST - tempTS[-1] + hiWin
maxST = tempST - tempTS[0] + loWin
p4.set_title("startTime %.1f Energy %.2f\nSlow %.1f chi2/ndf %.1f Min %d Max %d" % (st,en,slo,chi2NDF,minST,maxST))
p4.plot(M.trace('startTime')[:])
p4.set_ylabel('startTime')
p5.cla()
p5.plot(M.trace('energy')[:])
p5.set_ylabel('energy')
p6.cla()
p6.plot(M.trace('slowness')[:])
p6.set_ylabel('slowness')
plt.tight_layout()
plt.subplots_adjust(hspace=0.35)
plt.pause(scanSpeed)
def main(argv):
""" Get a sweet minimizer + time domain match filter working. Also graduate. """
scanSpeed = 1.
iList = -1
opt1 = ""
intMode = False
if (len(argv) >= 1): opt1 = argv[0]
if "-i" in (opt1): intMode = True
# Set input data and cuts
inputFile = TFile("~/project/match-skim/waveletSkimDS5_run23920.root") # calibration
# inputFile = TFile("~/project/v2-processwfs/waveletSkimDS5_90.root") # noisy BG
waveTree = inputFile.Get("skimTree")
theCut = inputFile.Get("cutUsedHere").GetTitle()
# theCut += " && waveS5/trapENFCal < 1200 && trapENFCal < 10"
theCut += " && trapENFCal < 30"
# Print cut and events passing cut
waveTree.Draw(">>elist", theCut, "entrylist")
elist = gDirectory.Get("elist")
waveTree.SetEntryList(elist)
nList = elist.GetN()
print "Using cut:\n",theCut,"\n"
print "Found",waveTree.GetEntries(),"input entries."
print "Found",nList,"entries passing cuts."
# Make a figure
fig = plt.figure(figsize=(15,10), facecolor='w')
p1 = plt.subplot2grid((6,7), (0,0), colspan=4, rowspan=3) # data & fit
p2 = plt.subplot2grid((6,7), (3,0), colspan=4, rowspan=3) # matched filter
p3 = plt.subplot2grid((6,7), (0,4), colspan=3, rowspan=2) # trace 1
p4 = plt.subplot2grid((6,7), (2,4), colspan=3, rowspan=2) # trace 2
p5 = plt.subplot2grid((6,7), (4,4), colspan=3, rowspan=2) # trace 3
plt.show(block=False)
# Make template(s)
tSamp, tR, tZ, tAmp, tST, tSlo = 5000, 0, 15, 100, 2500, 10
tOrig, tOrigTS = wl.MakeSiggenWaveform(tSamp,tR,tZ,tAmp,tST,tSlo)
# Loop over events
while True:
saveMe = False
iList += 1
if intMode==True and iList != 0:
value = raw_input()
if value=='q': break
if value=='s': saveMe=True
if value=='p': iList -= 2 # previous
if (value.isdigit()): iList = int(value) # go to entry
if iList >= elist.GetN(): break
entry = waveTree.GetEntryNumber(iList);
waveTree.LoadTree(entry)
waveTree.GetEntry(entry)
nChans = waveTree.channel.size()
numPass = waveTree.Draw("channel",theCut,"GOFF",1,iList)
chans = waveTree.GetV1()
chanList = list(set(int(chans[n]) for n in xrange(numPass)))
# Loop over hits passing cuts
hitList = (iH for iH in xrange(nChans) if waveTree.channel.at(iH) in chanList) # a 'generator expression'
for iH in hitList:
# ------------------------------------------------------------------------
# Load data
run = waveTree.run
chan = waveTree.channel.at(iH)
dataE = waveTree.trapENFCal.at(iH)
dataENM = waveTree.trapENM.at(iH)
# dataMax = waveTree.trapENMSample.at(iH)*10. - 4000
dataMax = waveTree.rt90.at(iH)
signal = wl.processWaveform(waveTree.MGTWaveforms.at(iH))
data = signal.GetWaveBLSub()
dataTS = signal.GetTS()
dataBL, dataNoise = signal.GetBaseNoise()
print "%d / %d Run %d nCh %d chan %d trapENF %.1f len %d" % (iList,nList,run,nChans,chan,dataE,len(data))
# Load and scale template
temp, tempTS = tOrig, tOrigTS
temp = temp * (dataENM / tAmp) # scale by amplitudes (not energies)
tempMax = np.argmax(temp) * 10 # convert to ns
tempTS = tempTS - (tempMax - dataMax) # align @ max of rising edge
tempMax = tempTS[np.argmax(temp)] # get the new max TS after the shifting
tempE = dataE # set 'calibrated' energy of template equal to data's trapENFCal.
# Lowpass or bandpass filter the data
# NOTE: This is tough. There might be a feature due to rising edges, between 3e6 and 5e6 Hz.
# But that's only from data. Doing it w/ siggen templates yielded squat.
# B,A = sig.butter(2, [3e6/(1e8/2),5e6/(1e8/2)], btype='bandpass')
B,A = sig.butter(2,1e6/(1e8/2),btype='lowpass') # nice lowpass filter
data_LowPass = sig.lfilter(B, A, data)
B1,A1 = sig.butter(2, [1e5/(1e8/2),1e6/(1e8/2)], btype='bandpass') # attempt at bandpass
data_BanPass = sig.lfilter(B1, A1, data)
# -- Run minimizers
# Set window and parameters
loWin, hiWin = dataTS[0], dataTS[-1]
mt, en, slo = dataMax-5, dataE+1, 20. # guesses
# print "guesses: mt %.0f en %.3f slo %.2f" % (mt, en, slo)
# pack into lists
InterpFn = interpolate.interp1d(tempTS, temp, kind="linear", copy="False", assume_sorted="True")
dataList = [data, dataTS, dataE, dataMax, loWin, hiWin, dataNoise]
tempList = [temp, tempTS, tempE, tempMax]
datas = [dataList, tempList, InterpFn]
floats = [mt,en,slo]
guess, guessTS = wm.MakeModel(dataList, tempList, floats, fn=InterpFn)
start = time.clock()
MakeTracesGlobal()
fitFail = False # you should output this to ROOT
# 0. brute - trying to make a quick initial guess for the slowness parameter
# FIXME: this keeps returning the lowest allowed value for slowness.
# bruteArgs = [en, datas]
# ranges = (slice(dataMax-500,dataMax+300,100), slice(1,100,10))
# resbrute = op.brute(bruteLnLike, ranges, args=(bruteArgs,), full_output=False, finish=None, disp=False)
# mt, slo = resbrute[0], resbrute[1]
# print "brute results: mt %.0f en %.3f slo %.2f" % (mt, en, slo)
# floats = [mt, en, slo]
# 1. nelder-mead (~0.5 sec). nobody does it better. works almost like magic.
result = op.minimize(findLnLike, floats, args=datas, method="Nelder-Mead")#,options={"maxiter":10})
if not result["success"]:
print "fit 'fail': ", result["message"]
fitFail = True
mt, en, slo = result["x"]
# print "nelder results: mt %.0f en %.3f slo %.2f" % (mt, en, slo)
nelder, nelderTS = wm.MakeModel(dataList, tempList, [mt,en,slo], fn=InterpFn)
nelderStop = time.clock()
# 2. powell "polish step" (~0.1 sec). Sometimes screws up Nelder's good results!
# floats = [mt,en,slo]
# powell = op.minimize(findLnLike, floats, args=datas, method="Powell")
# if not powell["success"]:
# fitFail= True
# print powell["message"]
# mt, en, slo = powell["x"]
# # print "powell results: mt %.0f en %.3f slo %.2f" % (mt, en, slo)
# model, modelTS = wm.MakeModel(dataList, tempList, [mt,en,slo], fn=InterpFn)
#
# powellStop = time.clock()
# print "Time: nelder %.3f powell %.3f total %.3f" % (nelderStop-start, powellStop-nelderStop, powellStop-start)
# take absolute values for parameters
mt, en, slo = abs(mt), abs(en), abs(slo)
model, modelTS = wm.MakeModel(dataList, tempList, [mt,en,slo], fn=InterpFn)
# compute a trap energy off the model (need pinghan's calibration constants)
trap = np.zeros(1000)
trap = np.append(trap,wl.trapezoidalFilter(model))
trapTS = modelTS
trapMax = np.amax(trap)
# -- Time domain match filter
match, matchTS = wm.MakeModel(dataList, tempList, [mt,en,slo], opt="nowindow")
match = np.flip(match,0)
# line up the max of the match with the max of the best-fit signal
modelMaxTime = modelTS[np.argmax(model)]
matchMaxTime = matchTS[np.argmax(match)]
matchTS = matchTS + (modelMaxTime - matchMaxTime)
idx = np.where((matchTS >= dataTS[0]-5) & (matchTS <= dataTS[-1]+5))
match, matchTS = match[idx], matchTS[idx]
# make sure match is same length as data, then compute convolution and parameters
matchMax, matchWidth, matchArea = 0, 9999, 0
smoothMF = np.zeros(len(dataTS))
if len(match)!=len(data):
print "array mismatch: len match %i len data %i " % (len(match),len(data))
else:
# I can't decide which of these is better.
# smoothMF = gaussian_filter(match * data, sigma=float(5))
smoothMF = gaussian_filter(match * data_LowPass,sigma=float(5))
# computer AWESOME match filter parameters
matchMax = np.amax(smoothMF)
idx = np.where(smoothMF > matchMax/2.)
matchWidth = matchTS[idx][-1] - matchTS[idx][0]
matchArea = np.sum(match[idx]) / float(len(match[idx]))
# Plot data and template
p1.cla()
p1.plot(dataTS,data,'b',label='data')
idx2 = np.where((tempTS >= dataTS[0]-5) & (tempTS <= dataTS[-1]+5))
p1.plot(tempTS[idx2],temp[idx2],'r',label='template')
# p1.plot(dataTS, data_LowPass, label='lowpass')
# p1.plot(dataTS, data_BanPass, label='bandpass')
p1.plot(trapTS,trap,color='k',label='bestfit-trap')
p1.plot(nelderTS,nelder,color='cyan',label='bestfit')
# p1.plot(modelTS,model,color='magenta',label='powells')
p1.set_xlabel('Time (s)')
p1.set_ylabel('Voltage (arb)')
p1.set_title("Run %i Ch %i E %.2f ENM %.2f trapMax %.2f" % (run,chan,dataE,dataENM,trapMax))
p1.legend(loc=4)
p2.cla()
p2.plot(dataTS,data,'b',alpha=0.8,label='data')
# p2.plot(guessTS,guess,'y',alpha=0.8,label='guess')
p2.plot(matchTS,match,'k',label='match')
p2.plot(modelTS,model,color='orange',label='model')
p2.plot(dataTS,data_LowPass,'r',label='lowpass')
if len(match)==len(data): p2.plot(matchTS,smoothMF,'g',label='smoothMF')
p2.axvline(matchTS[idx][-1],color='green',alpha=0.7)
p2.axvline(matchTS[idx][0],color='green',alpha=0.7)
p2.set_title("mMax %.2f mWidth %.2f mAreaNorm %.2f mM/mW %.4f" % (matchMax,matchWidth,matchArea,matchMax/matchWidth))
p2.legend(loc=4)
# plot traces
p3.cla()
p3.set_title("maxTime %.1f Energy %.2f Slow %.1f" % (mt,en,slo))
p3.plot(mtTrace[1:])
p3.set_ylabel('maxTime')
p4.cla()
p4.plot(enTrace[1:])
p4.set_ylabel('energy')
p5.cla()
p5.plot(sloTrace[1:])
p5.set_ylabel('slowness')
plt.tight_layout()
plt.pause(scanSpeed)