def compareShapes(h1,h2,outFile,xTitle="",yTitle="",yRange=[],xRange=[],log=False,label1="",label2="",labelR="Data/MC",data=False):
hRpf_mj = createRatio(h1,h2)
hRatio = []
hRatioErrors = []
hDataErrors = []
hData = []
hDataCentres = []
for i in range(1,hRpf_mj.GetNbinsX()+1):
hRatio.append(hRpf_mj.GetBinContent(i))
hRatioErrors.append(hRpf_mj.GetBinError(i))
for i in range(1,h2.GetNbinsX()+1):
hData.append(h2.GetBinContent(i))
hDataCentres.append(h2.GetBinCenter(i))
hDataErrors.append(h2.GetBinError(i))
#numpy histograms
h1, h1Edges = hist2array(h1,return_edges=True)
h2, h2Edges = hist2array(h2,return_edges=True)
hRatio = np.asarray(hRatio)
hRatioErrors = np.asarray(hRatioErrors)
centresRatio = (h1Edges[0][:-1] + h1Edges[0][1:])/2.
plt.style.use([hep.style.CMS])
f, axs = plt.subplots(2,1, sharex=True, sharey=False,gridspec_kw={'height_ratios': [4, 1],'hspace': 0.05})
axs = axs.flatten()
plt.sca(axs[0])
if(log):
axs[0].set_yscale("log")
hep.histplot(h1,h1Edges[0],stack=False,ax=axs[0],label = label1, histtype="step",color="r")
if(label2=="data_obs"):
print("Plotting data")
plt.errorbar(hDataCentres,hData, yerr=hDataErrors, fmt='o',color="k",label = label2)
else:
hep.histplot(h2,h2Edges[0],stack=False,ax=axs[0],label = label2, histtype="step",color="k")
plt.ylabel(yTitle, horizontalalignment='right', y=1.0)
axs[0].legend()
axs[1].set_xlabel(xTitle)
#axs[0].set_ylabel(yTitle)
axs[1].set_ylabel(labelR)
if(yRange):
axs[0].set_ylim(yRange)
if(xRange):
axs[0].set_xlim(xRange)
if data:
hep.cms.text("WiP",loc=1)
hep.cms.lumitext(text='59.8 $fb^{-1} (13 TeV)$', ax=axs[0], fontname=None, fontsize=None)
else:
hep.cms.lumitext(text='2018', ax=axs[0], fontname=None, fontsize=None)
hep.cms.text("Simulation WiP",loc=1)
plt.legend(loc="best")#loc = (0.4,0.2))
plt.sca(axs[1])#switch to lower pad
axs[1].axhline(y=1.0, xmin=0, xmax=1, color="r")
axs[1].set_ylim([0.0,2.0])
plt.xlabel(xTitle, horizontalalignment='right', x=1.0)
plt.errorbar(centresRatio,hRatio, yerr=hRatioErrors, fmt='o',color="k")
print("Saving {0}".format(outFile))
plt.savefig(outFile)
def check_array2hist(hist):
shape = np.array([hist.GetNbinsX(), hist.GetNbinsY(), hist.GetNbinsZ()])
shape = shape[:hist.GetDimension()]
arr = RNG.randint(0, 10, size=shape)
rnp.array2hist(arr, hist)
arr_hist = rnp.hist2array(hist)
assert_array_equal(arr_hist, arr)
shape_overflow = shape + 2
arr_overflow = RNG.randint(0, 10, size=shape_overflow)
hist_overflow = hist.Clone()
hist_overflow.Reset()
rnp.array2hist(arr_overflow, hist_overflow)
arr_hist_overflow = rnp.hist2array(hist_overflow, include_overflow=True)
assert_array_equal(arr_hist_overflow, arr_overflow)
if len(shape) == 1:
return
# overflow not specified on all axes
arr_overflow2 = arr_overflow[1:-1]
hist_overflow2 = hist.Clone()
hist_overflow2.Reset()
rnp.array2hist(arr_overflow2, hist_overflow2)
arr_hist_overflow2 = rnp.hist2array(hist_overflow2, include_overflow=True)
assert_array_equal(arr_hist_overflow2[1:-1], arr_overflow2)
def getMiniGroupHists(lpgbt_hists, minigroups_swap, root=False):
minigroup_hists = []
minigroup_hists_inclusive = {}
minigroup_hists_phi60 = {}
for minigroup, lpgbts in minigroups_swap.items():
inclusive = ROOT.TH1D(
"minigroup_ROverZ_silicon_" + str(minigroup) + "_0", "", 42, 0.076,
0.58)
phi60 = ROOT.TH1D("minigroup_ROverZ_silicon_" + str(minigroup) + "_1",
"", 42, 0.076, 0.58)
for lpgbt in lpgbts:
inclusive.Add(lpgbt_hists[0][lpgbt])
phi60.Add(lpgbt_hists[1][lpgbt])
inclusive_array = hist2array(inclusive)
phi60_array = hist2array(phi60)
if (root):
minigroup_hists_inclusive[minigroup] = inclusive
minigroup_hists_phi60[minigroup] = phi60
else:
minigroup_hists_inclusive[minigroup] = inclusive_array
minigroup_hists_phi60[minigroup] = phi60_array
minigroup_hists.append(minigroup_hists_inclusive)
minigroup_hists.append(minigroup_hists_phi60)
return minigroup_hists
def compare(shared_paths, pr_flat_dict, base_flat_dict, paths_to_save_in_pr, paths_to_save_in_base):
# Collect paths that have to be written to both output files
for path in shared_paths:
pr_item = pr_flat_dict[path]
base_item = base_flat_dict[path]
if pr_item == None or base_item == None:
continue
are_different=False
if pr_item.InheritsFrom('TProfile2D') and base_item.InheritsFrom('TProfile2D'):
# Compare TProfile (content, entries and errors)
are_different = not compare_TProfile(pr_item, base_item)
elif pr_item.InheritsFrom('TProfile') and base_item.InheritsFrom('TProfile'):
# Compare TProfile (content, entries and errors)
are_different = not compare_TProfile(pr_item, base_item)
elif pr_item.InheritsFrom('TH1') and base_item.InheritsFrom('TH1'):
# Compare bin by bin
pr_array = root_numpy.hist2array(hist=pr_item, include_overflow=True, copy=False)
base_array = root_numpy.hist2array(hist=base_item, include_overflow=True, copy=False)
if pr_array.shape != base_array.shape or not np.allclose(pr_array, base_array, equal_nan=True):
are_different = True
else:
# Compare non histograms
if pr_item != base_item:
are_different = True
if are_different:
paths_to_save_in_pr.append(path)
paths_to_save_in_base.append(path)
def root_to_template(root_name,
file_name,
histogram_names=None,
metadata={
"version": "0.0",
"date": datetime.now().strftime('%Y%m%d_%H:%M:%S')
}):
if not HAVE_ROOT:
raise NotImplementedError("root_to_template requires ROOT, root_numpy")
froot = rt.TFile(root_name)
if histogram_names is None:
histogram_names = []
for k in froot.GetListOfKeys():
if froot.Get(k.GetName()).InheritsFrom("TH1"):
histogram_names.append(k.GetName())
_, bins = root_numpy.hist2array(froot.Get(histogram_names[0]),
return_edges=True)
axis_names = get_root_hist_axis_labels(froot.Get(histogram_names[0]))
histograms = []
for histogram_name in histogram_names:
histogram, _ = root_numpy.hist2array(froot.Get(histogram_name),
return_edges=True)
histograms.append(histogram)
numpy_to_template(bins,
histograms,
file_name,
histogram_names=histogram_names,
axis_names=axis_names,
metadata=metadata)
def check_array2hist(hist):
shape = np.array([hist.GetNbinsX(), hist.GetNbinsY(), hist.GetNbinsZ()])
shape = shape[:hist.GetDimension()]
arr = RNG.randint(0, 10, size=shape)
rnp.array2hist(arr, hist)
arr_hist = rnp.hist2array(hist)
assert_array_equal(arr_hist, arr)
shape_overflow = shape + 2
arr_overflow = RNG.randint(0, 10, size=shape_overflow)
hist_overflow = hist.Clone()
hist_overflow.Reset()
rnp.array2hist(arr_overflow, hist_overflow)
arr_hist_overflow = rnp.hist2array(hist_overflow, include_overflow=True)
assert_array_equal(arr_hist_overflow, arr_overflow)
if len(shape) == 1:
return
# overflow not specified on all axes
arr_overflow2 = arr_overflow[1:-1]
hist_overflow2 = hist.Clone()
hist_overflow2.Reset()
rnp.array2hist(arr_overflow2, hist_overflow2)
arr_hist_overflow2 = rnp.hist2array(hist_overflow2, include_overflow=True)
assert_array_equal(arr_hist_overflow2[1:-1], arr_overflow2)
def correct_bbb(hist, vorig, funcname, normname=''):
if vorig == 'mllVSmth_4x3':
# 4 mth x 3 mll ([10, 40, 55, 210])
vfolding = [range(i, i + 12, 3) for i in range(3)]
vmapping = [0, 0, 1, 1, 2, 2]
elif vorig == 'mllVSmth_3x3':
# [10, 40, 70, 210]
vfolding = [range(i, i + 9, 3) for i in range(3)]
vmapping = [0, 0, 1, 1, 2, 2]
elif vorig == 'mllVSmth_2x2':
# [10, 50, 210]
vfolding = [range(i, i + 4, 2) for i in range(2)]
vmapping = [0, 0, 0, 1, 1, 1]
postfit_full = common.make_roofit_histogram('postfit',
postfit_ws,
funcname,
normname=normname,
fold=vfolding)
postfit_nobbb = common.make_roofit_histogram('prefit',
nobbb_ws,
funcname,
normname=normname,
fold=vfolding)
cont = rnp.hist2array(hist, copy=False)
cont *= (rnp.hist2array(postfit_full, copy=False) /
rnp.hist2array(postfit_nobbb, copy=False))[np.array(vmapping)]
postfit_full.Delete()
postfit_nobbb.Delete()
def makeMCTruthDataset(data, etas, pts, masses):
#add charge for mc truth events
charge1 = np.ones_like(data['eta1'])
charge2 = -np.ones_like(data['eta1'])
datasetMCTruth = np.array([np.concatenate((data['eta1'],data['eta2']),axis=None),np.concatenate((charge1*data['mcpt1'],charge2*data['mcpt2']),axis=None),np.concatenate((data['res1'], data['res2']),axis=None)])
histoMCTruth, edges = np.histogramdd(datasetMCTruth.T, bins = [etas,pts,masses])
good_idx = np.nonzero(np.sum(histoMCTruth,axis=-1)>100.)
histoMCTruth = histoMCTruth[good_idx]
#compute mean in each bin (integrating over mass) for pt-dependent terms
massesfull = np.array([masses[0],masses[-1]])
histoden = np.histogramdd(datasetMCTruth.T, bins = [etas,pts,massesfull])[0][good_idx]
k = 1./datasetMCTruth[1]
eta = datasetMCTruth[0]
sEta = np.sin(2*np.arctan(np.exp(-eta)))
L = computeTrackLength(eta)
fIn = ROOT.TFile.Open("resolutionMCtruth.root")
bHisto = fIn.Get("b")
dHisto = fIn.Get("d")
bterm = hist2array(bHisto)
dterm = hist2array(dHisto)
terms_etas = np.linspace(-2.4, 2.4, bterm.shape[0]+1, dtype='float64')
findBin = np.digitize(eta, terms_etas)-1
b = bterm[findBin]
d = dterm[findBin]
terms = []
terms.append(1./k)
terms.append(np.abs(sEta*k))
terms.append(1./np.square(k))
terms.append(np.square(L))
#terms.append(b*np.square(L)*np.reciprocal(1.+d/np.square(pt)/np.square(L)))
terms.append(np.square(k))
means = []
for term in terms:
histoterm = np.histogramdd(datasetMCTruth.T, bins = [etas,pts,massesfull], weights=term)[0][good_idx]
ret = histoterm/histoden
#remove spurious mass dimension
ret = np.squeeze(ret, axis=-1)
means.append(ret.flatten())
mean = np.stack(means,axis=-1)
pkg = {}
pkg['dataset'] = histoMCTruth
pkg['edges'] = edges
pkg['binCenters'] = mean
pkg['good_idx'] = good_idx
return pkg
def check_hist2array_THnSparse(hist):
hist_thnsparse = ROOT.THnSparse.CreateSparse("", "", hist)
array = rnp.hist2array(hist)
array_thnsparse = rnp.hist2array(hist_thnsparse)
# non-zero elements
assert_true(np.any(array))
# arrays should be identical
assert_array_equal(array, array_thnsparse)
def check_hist2array_THn(hist):
hist_thn = ROOT.THn.CreateHn("", "", hist)
array = rnp.hist2array(hist)
array_thn = rnp.hist2array(hist_thn)
# non-zero elements
assert_true(np.any(array))
# arrays should be identical
assert_array_equal(array, array_thn)
def check_hist2array_THn(hist):
hist_thn = ROOT.THn.CreateHn("", "", hist)
array = rnp.hist2array(hist)
array_thn = rnp.hist2array(hist_thn)
# non-zero elements
assert_true(np.any(array))
# arrays should be identical
assert_array_equal(array, array_thn)
def check_hist2array_THnSparse(hist):
hist_thnsparse = ROOT.THnSparse.CreateSparse("", "", hist)
array = rnp.hist2array(hist)
array_thnsparse = rnp.hist2array(hist_thnsparse)
# non-zero elements
assert_true(np.any(array))
# arrays should be identical
assert_array_equal(array, array_thnsparse)
def plotSidebandsMJY_mpl(h_3d,outFile,xTitle="",yTitle="",yRange=[],xRange=[],log=False):
nBinsX = h_3d.GetNbinsX()
nBinsY = h_3d.GetNbinsY()
nBinsZ = h_3d.GetNbinsZ()
wp = 0.8
point = 0.0
taggerLowBin = h_3d.GetXaxis().FindBin(point)
taggerHighBin = h_3d.GetXaxis().FindBin(wp) - 1
h_mj_fail = h_3d.ProjectionZ("mj_failProjection" ,taggerLowBin,taggerHighBin,1,nBinsY)
h_mj_pass = h_3d.ProjectionZ("mj_passProjection" ,taggerHighBin,nBinsX,1,nBinsY)
h_mj_fail.Scale(1/h_mj_fail.Integral())
h_mj_pass.Scale(1/h_mj_pass.Integral())
h_mj_pass.Rebin(2)
h_mj_fail.Rebin(2)
hRpf_mj = createRatio(h_mj_pass,h_mj_fail)
hRatio = []
hRatioErrors = []
for i in range(1,hRpf_mj.GetNbinsX()+1):
hRatio.append(hRpf_mj.GetBinContent(i))
hRatioErrors.append(hRpf_mj.GetBinError(i))
#numpy histograms
hMJYFail, hMJYFailEdges = hist2array(h_mj_fail,return_edges=True)
hMJYPass, hMJYPassEdges = hist2array(h_mj_pass,return_edges=True)
hRatio = np.asarray(hRatio)
hRatioErrors = np.asarray(hRatioErrors)
centresRatio = (hMJYPassEdges[0][:-1] + hMJYPassEdges[0][1:])/2.
plt.style.use([hep.style.CMS])
f, axs = plt.subplots(2,1, sharex=True, sharey=False,gridspec_kw={'height_ratios': [4, 1],'hspace': 0.05})
axs = axs.flatten()
plt.sca(axs[0])
if(log):
axs[0].set_yscale("log")
hep.histplot(hMJYPass,hMJYPassEdges[0],stack=False,ax=axs[0],label = "Pass", histtype="step",color="r")
hep.histplot(hMJYFail,hMJYFailEdges[0],stack=False,ax=axs[0],label = "Fail", histtype="step",color="b")
axs[0].legend()
axs[1].set_xlabel(xTitle)
axs[0].set_ylabel(yTitle)
axs[1].set_ylabel("Data/MC")
plt.ylabel(yTitle, horizontalalignment='right', x=1.0)
if(yRange):
axs[0].set_ylim(yRange)
if(xRange):
axs[0].set_xlim(xRange)
hep.cms.lumitext(text='59.8 $fb^{-1} (13 TeV)$', ax=axs[0], fontname=None, fontsize=None)
hep.cms.text("Simulation WiP",loc=1)
plt.legend(loc="best")#loc = (0.4,0.2))
plt.sca(axs[1])#switch to lower pad
axs[1].axhline(y=1.0, xmin=0, xmax=1, color="r")
axs[1].set_ylim([0.0,2.0])
plt.xlabel(xTitle, horizontalalignment='right', x=1.0)
plt.errorbar(centresRatio,hRatio, yerr=hRatioErrors, fmt='o',color="k")
print("Saving {0}".format(outFile))
plt.savefig(outFile)
def add_hist(total, hist):
if args.combination_sideways:
nx = hist.GetNbinsX()
first, last = nx * isource, nx * (isource + 1)
tc = rnp.hist2array(total, copy=False)
tc[first:last] += rnp.hist2array(hist, copy=False)
te2 = rnp.array(total.GetSumw2(), copy=False)[1:-1]
te2[first:last] += rnp.array(hist.GetSumw2(), copy=False)[1:-1]
else:
total.Add(hist)
def addHist(self, histname):
histogram = self.file.Get(histname)
if len(self.data) == 0:
self.data = np.atleast_2d(rp.hist2array(histogram))
self.bin_edges = getBinEdges(histogram)
else:
data_new = np.empty((self.data.shape[0] + 1, self.data.shape[1]))
data_new[-1, :] = rp.hist2array(histogram)
data_new[:-1, :] = self.data
self.data = data_new
def get_data(folder, fname, drift_margin = 0, crop = True, blur = None,
white_noise = 0, coherent_noise = 0):
print 'Reading', fname
try:
if isinstance(folder, TFile): # read from ROOT file
A_raw = hist2array(folder.Get(fname + '_raw'))
A_deposit = hist2array(folder.Get(fname + '_deposit'))
A_pdg = hist2array(folder.Get(fname + '_pdg'))
else: # read text files
A_raw = np.genfromtxt(folder+'/'+fname + '.raw', delimiter=' ',
dtype=np.float32)
A_deposit = np.genfromtxt(folder+'/'+fname + '.deposit',
delimiter=' ', dtype=np.float32)
A_pdg = np.genfromtxt(folder+'/'+fname + '.pdg', delimiter=' ',
dtype=np.int32)
except:
print 'Bad event, return empty arrays'
return None, None, None, None, None
if A_raw.shape[0] < 8 or A_raw.shape[1] < 8:
return None, None, None, None, None
test_pdg = np.sum(A_pdg)
test_dep = np.sum(A_deposit)
test_raw = np.sum(A_raw)
if test_raw == 0.0 or test_dep == 0.0 or test_pdg == 0:
return None, None, None, None, None
print test_raw, test_dep, test_pdg
#assert np.sum(A_deposit) > 0
# get main event body (99% signal)
if crop:
evt_start_ind, evt_stop_ind = get_event_bounds(A_deposit, drift_margin)
A_raw = A_raw[:,evt_start_ind:evt_stop_ind]
A_deposit = A_deposit[:,evt_start_ind:evt_stop_ind]
A_pdg = A_pdg[:,evt_start_ind:evt_stop_ind]
else:
evt_start_ind = 0
evt_stop_ind = A_raw.shape[1]
print evt_start_ind, evt_stop_ind
A_raw = applyBlur(A_raw, blur)
A_raw = addWhiteNoise(A_raw, white_noise)
A_raw = addCoherentNoise(A_raw, coherent_noise)
deposit_th_ind = A_deposit < 2.0e-5
A_pdg[deposit_th_ind] = 0
tracks = A_pdg.copy()
showers = A_pdg.copy()
tracks[(A_pdg & 0x0FFF) == 11] = 0
tracks[tracks > 0] = 1
showers[(A_pdg & 0x0FFF) != 11] = 0
showers[showers > 0] = 1
return A_raw, A_deposit, A_pdg, tracks, showers
def read_decorr(self):
myfile = root_open(self.filename, 'read')
awesome = myfile.Get(self.directory)
cumu_dW2TwoTwoD = rnp.hist2array(
awesome.Get('cumulants').Get('mixed').Get('dW2TwoTwoD').Get(
'cumu_dW2TwoTwoD'))
cumu_dW2TwoTwoN = rnp.hist2array(
awesome.Get('cumulants').Get('mixed').Get('dW2TwoTwoN').Get(
'cumu_dW2TwoTwoN'))
self.differential_mixedn[..., dW2TwoTwoD] = cumu_dW2TwoTwoD
self.differential_mixedn[..., dW2TwoTwoN] = cumu_dW2TwoTwoN
def get_efficiency(title1, title2):
#nPV_reconstructed
nums1, edges1 = rn.hist2array(title1, return_edges=True, copy=True)
n_ed = np.sum(nums1)
#nPV_reconstructible
nums2, edges2 = rn.hist2array(title2, return_edges=True, copy=True)
n_ible = np.sum(nums2)
efficiency = n_ed / n_ible
return efficiency
def get_hists(filename):
import sys
sys.argv.append('-b')
from ROOT import TFile
from root_numpy import hist2array
f = TFile(filename, 'READ')
h_ep = f.Get('gem_efficiency_ep')
h_ee = f.Get('gem_efficiency_ee')
hist_ep, edges = hist2array(h_ep, return_edges=True)
hist_ee, edges = hist2array(h_ee, return_edges=True)
return hist_ep[1:], hist_ee[1:], edges[0][1:]
def Saver(bkgfilename, sgfilename, B_events, S_events):
sig = ROOT.TFile.Open(sgfilename)
bkg = ROOT.TFile.Open(bkgfilename)
Nbkg = len(bkg.GetListOfKeys())
Nsig = len(sig.GetListOfKeys())
bkgArray = []
sigArray = []
bkg_iteration = random.sample(xrange(0, Nbkg), B_events)
sig_iteration = random.sample(xrange(0, Nsig), S_events)
#print(bkg_iteration)
countBKG = 0
countSig = 0
RangeSig = [0, Nsig, int(math.floor(Nsig / S_events))]
for i in range(0, Nbkg, int(math.floor(Nbkg / B_events))):
histoname = "histo" + str(i)
aHisto = bkg.Get(histoname)
aHisto.Print() #This prevents all the array elements being 0.
#print("BKG")
anArrayfromHisto = root_numpy.hist2array(aHisto)
anArrayfromHisto = np.rot90(anArrayfromHisto)
bkgArray.append(anArrayfromHisto)
countBKG = countBKG + 1
print(countBKG)
for i in range(0, Nsig, int(math.floor(Nsig / S_events))):
histoname = "histo" + str(i)
aHisto = sig.Get(histoname)
aHisto.Print() #This prevents all the array elements being 0.
#print("SIG")
anArrayfromHisto = root_numpy.hist2array(aHisto)
anArrayfromHisto = np.rot90(anArrayfromHisto)
if np.sum(anArrayfromHisto) != 0.0:
sigArray.append(anArrayfromHisto)
countSig = countSig + 1
print(countSig)
bkgArray = np.array(bkgArray)
sigArray = np.array(sigArray)
print(countBKG)
print(countSig)
return bkgArray, sigArray
def extract_hist(directory, process_dict, total_signal_list, total_background_list, total_list):
for key in directory.GetListOfKeys():
print(key.GetName())
subdir = directory.Get(key.GetName())
for subkey in subdir.GetListOfKeys():
print(subkey.GetName())
print(subkey.GetName() == "total_signal")
if subkey.GetName() == "data": continue
hist = subdir.Get(subkey.GetName())
if "total" not in subkey.GetName():
if subkey.GetName() not in process_dict.keys(): process_dict[subkey.GetName()] = []
process_dict[subkey.GetName()] = np.append(process_dict[subkey.GetName()], root_numpy.hist2array(hist))
elif subkey.GetName() == "total_signal": total_signal_list.append(list(root_numpy.hist2array(hist)))
elif subkey.GetName() == "total_background": total_background_list.append(list(root_numpy.hist2array(hist)))
elif subkey.GetName() == "total": total_list.append(list(root_numpy.hist2array(hist)))
def getErrors(default, others):
dfarr = root_numpy.hist2array(default)
errs = np.zeros(len(dfarr))
for other in others:
if type(other) == list:
err1 = root_numpy.hist2array(other[0]) - dfarr
err1 = err1**2
err2 = root_numpy.hist2array(other[1]) - dfarr
err2 = err2**2
err = np.maximum(err1, err2)
errs += err
else:
err = root_numpy.hist2array(other) - dfarr
err = err**2
errs += err
return errs
def get_max_res_map(fname):
"""Get the histogram showing the acceptance of the detector at maximal resolution"""
with root_open(fname) as f:
h = list(f.c2_correlations)[0][-1]
if h.GetName() != "etaPhiZvtx_max_res":
raise ValueError("Histogram order is different than expected")
return root_numpy.hist2array(h, return_edges=True)
def makeForwardPlotsSum(awesome, Zinit, mydata, doedges, dofill):
histname = 'NUAforward'
z = hist2array(awesome.FindObject('EventInfo').FindObject('Vertex'))
zbins = 10
Zinit = np.nansum(Zinit, axis=2)
z = np.nansum(z)
Znorm = nua_norm(Zinit, z)
myplot(Znorm[:, :], mydata + '/forward/nua_norm', '',
r'$dN / d\varphi d\eta$', False, -1, 'FMD')
myplot(Znorm[:, :], mydata + '/forward/nua_norm_wfill', 'w. fills',
r'$dN_{ch} / d\eta d\varphi$', False, -1, 'FMD')
Zmean = nua_meanSum(Znorm)
Znew = nua_frac(Zmean, Znorm)
Zmean[Zmean == 0] = np.nan
myplot(Zmean[:, :], mydata + '/forward/nua_mean_wfill', '',
r'$\langle N_{ch} \rangle / d\eta$', False, -1, 'FMD')
myplot(Znew[:, :], mydata + '/forward/nua_frac', '',
r'$\langle N \rangle / N$', False, -1, 'FMD')
plt.show()
Zres = nua_result(Znew, Znorm)
Zforward = Znew
myplot(Zres[:, :], mydata + '/forward/nua_res', '',
r'$\langle N \rangle / N$', False, -1, 'FMD')
return Zforward
def get_curve(self, observable=None, norm=1, npoints=1000):
""" Get projection of the pdf curve
Args:
observable (str, optional): Name of the observable
norm (float, optional): normalisation for the pdf, default=1
npoints (int): number of points, default=1000
Returns:
hx, hy : numpy arrays of x and y points of the pdf projection
Examples:
>>> import matplotlib.pyplot as plt
>>> plt.plot(*pdf.get_curve())
"""
import root_numpy
import numpy as np
if observable is not None:
assert isinstance(observable,
str), "please specify the name of the observable"
assert observable in self.observables, "observable not found"
else:
observable = self.get_observable().GetName()
h = self.roo_pdf.createHistogram(observable, npoints)
hy, hx = root_numpy.hist2array(h, False, False, True)
# Normalise y
hy = npoints * hy / np.sum(hy)
# center x
hx = (hx[0][:-1] + hx[0][1:]) / 2.
return hx, np.multiply(hy, norm)
def getErrors(default, others, keys):
dfarr = root_numpy.hist2array(default)
errs = {}
for other, key in zip(others, keys):
if type(other) == list:
err1 = root_numpy.hist2array(other[0]) - dfarr
err1 = abs(err1)
err2 = root_numpy.hist2array(other[1]) - dfarr
err2 = abs(err2)
err = numpy.maximum(err1, err2)
errs[key] = err
else:
err = root_numpy.hist2array(other) - dfarr
err = abs(err)
errs[key] = err
return errs
def convert_histos(root_files, hist):
global input_dir
# Set histogram directory prefix based on ECAL subdetector
if hist.startswith("EB"):
hist_name = 'EcalBarrel/Run summary/%s' % hist
else:
hist_name = 'EcalEndcap/Run summary/%s' % hist
hists = []
for root_file in root_files:
histo = root_file.Get(
'DQMData/Run %d/%s' % (run, hist_name)
) # Get list of associated ROOT histograms (ROOT::TH2F or ROOT::TProfile2D)
try:
histo.Scale(1 / histo.GetBinContent(
histo.GetMaximumBin())) #Normalize Histograms by its max
hists.append(histo)
except ZeroDivisionError:
print "Empty histogram: ", hist, " in file: ", root_file
except AttributeError:
print "Empty root filr: ", root_file
X = np.stack([hist2array(hist).T for hist in hists
]) # Convert ROOT histograms to NumPy arrays and stack
return X
def __init__(self, options):
self.rebin = options.rebin
self.options = options
self.pedfile_fullres_name = options.pedfile_fullres_name
self.tmpname = options.tmpname
geometryPSet = open(
'modules_config/geometry_{det}.txt'.format(det=options.geometry),
'r')
geometryParams = eval(geometryPSet.read())
self.cg = cameraGeometry(geometryParams)
self.xmax = self.cg.npixx
if not os.path.exists(self.pedfile_fullres_name):
print("WARNING: pedestal file with full resolution ",
self.pedfile_fullres_name,
" not existing. First calculate them...")
self.calcPedestal(options, 1)
if not options.justPedestal:
print("Pulling pedestals...")
# first the one for clustering with rebin
ctools = cameraTools(self.cg)
# then the full resolution one
pedrf_fr = ROOT.TFile.Open(self.pedfile_fullres_name)
self.pedmap_fr = pedrf_fr.Get('pedmap').Clone()
self.pedmap_fr.SetDirectory(0)
self.pedarr_fr = hist2array(self.pedmap_fr).T
self.noisearr_fr = ctools.noisearray(self.pedmap_fr).T
pedrf_fr.Close()
if options.vignetteCorr:
self.vignmap = ctools.loadVignettingMap()
else:
self.vignmap = np.ones((self.xmax, self.xmax))
def magnify_dump(ctx, out, filename):
'''Dump magnify histograms into Numpy .npz files.
The underlying histogram array is dumped into an array of the same
name. For every dimension of histogram an array of bin edges is
dumped as <name>_<dim>edges where <dim> is "x", "y" or "z".
'''
import ROOT
import numpy
from root_numpy import hist2array
from time import time
print "Reading ROOT file"
t1 = time()
arrs = dict()
tfile = ROOT.TFile.Open(filename)
for key in tfile.GetListOfKeys():
cname = key.GetClassName()
if cname[:3] not in ["TH1", "TH2", "TH3"]:
continue
th = key.ReadObj()
hname = th.GetName()
arr, edges = hist2array(th, return_edges=True)
arrs[hname] = arr
for dim, edge in enumerate(edges):
arrs["%s_%sedge" % (hname, "xyz"[dim])] = edge
t2 = time()
print t2 - t1 # takes 5.7 seconds compared to 5.3 seconds loading npz
print "Writing NPZ file"
numpy.savez_compressed(out, **arrs)
t3 = time()
print t3 - t2
def channel_responses(ctx, tscale, scale, name, infile, outfile):
'''Produce the per-channel calibrated response JSON file from a TH2D
of the given name in the input ROOT file provided by the analysis.
- tscale :: a number to multiply to the time axis of the histogram
in order to bring the result into the WCT system of units. It
may be expressed as a string of an algebraic expression which
includes symbols, eg "0.5*us".
- scale :: a number multiplied to all samples in the histogram in
order to make the sample value a unitless relative measure. It
may be expressed as a string of an algebraic expression which
includes symbols, eg "0.5*us". For uBoone's initial
20171006_responseWaveforms.root the appropriate scale is
1e-9*0.5/1.13312 = 4.41267e-10
'''
import json
import ROOT
import numpy
from root_numpy import hist2array
tscale = eval(tscale, units.__dict__)
scale = eval(scale, units.__dict__)
tf = ROOT.TFile.Open(str(infile))
assert(tf)
h = tf.Get(str(name))
if not h:
click.echo('Failed to get histogram "%s" from %s' % (name, infile))
sys.exit(1)
arr,edges = hist2array(h, return_edges=True)
arr *= scale
tedges = edges[1]
t0,t1 = tscale*(tedges[0:2])
tick = t1-t0
nchans, nticks = arr.shape
channels = list()
for ch in range(nchans):
# reduce down to ~32 bit float precision to save file space
res = [float("%.6g"%x) for x in arr[ch,:].tolist()]
one = [ch, res]
channels.append(one)
dat = dict(tick=tick, t0=t0, channels=channels)
jtext = json.dumps(dat, indent=4)
if outfile.endswith(".json.bz2"):
import bz2
bz2.BZ2File(outfile, 'w').write(jtext)
return
if outfile.endswith(".json.gz"):
import gzip
gzip.open(outfile, 'wb').write(jtext) # wb?
return
open(outfile, 'w').write(jtext)
return
def loadVignettingMap(self):
print("Loading vignette map from: {vf}...".format(
vf=self.geometry.vignette))
det = self.geometry.name
if det == 'lemon': # not implemented (we were taking the efficienct region within the FC)
return self.vignetteMap[det]
elif det == 'lime' or 'Mango_full':
if not self.vignetteMap[det].any():
tf = ROOT.TFile.Open(self.geometry.vignette)
hmap = tf.Get('normmap_lime')
vignetteMapRebinned = hist2array(hmap)
tf.Close()
rebinx = int(self.geometry.npixx /
vignetteMapRebinned.shape[0])
rebiny = int(self.geometry.npixx /
vignetteMapRebinned.shape[1])
macroPixel = np.zeros((rebinx, rebiny))
print("Macro-pixel of the vignetting map has size = ",
macroPixel.shape)
for ibx in range(vignetteMapRebinned.shape[0]):
for iby in range(vignetteMapRebinned.shape[1]):
macroPixel[:, :] = 1. / vignetteMapRebinned[iby, ibx]
(self.vignetteMap[det]
)[int(ibx * rebinx):int((ibx + 1) * rebinx),
int(iby * rebiny):int((iby + 1) *
rebiny)] = macroPixel
return self.vignetteMap[det]
else:
return self.vignetteMap[det]
else:
print('WARNING! Geometry ', det,
' not foreseen. Return correction 1')
return self.vignetteMap[det]
def getProfile2DataRaw(root_file, root_folder, coll_name):
print "opening...", root_file
# open root file
profile_file = TFile(root_file)
# get data
profile_data = profile_file.Get(root_folder + coll_name) #print histdata
# get dimension, sums and x,y-positions. Note: using hist2array for Th2profile data
sums, edges = hist2array(profile_data,
include_overflow=False,
return_edges=True) #print counts, edge
# get contents
contents = np.zeros(shape=np.shape(sums))
for y_index, y_value in enumerate(sums[0]):
for x_index, x_value in enumerate(sums.T[0]):
contents[x_index][y_index] = profile_data.GetBinContent(
x_index + 1, y_index + 1)
# get errors
errors = np.zeros(shape=np.shape(sums))
for y_index, y_value in enumerate(sums[0]):
for x_index, x_value in enumerate(sums.T[0]):
errors[x_index][y_index] = profile_data.GetBinError(
x_index + 1, y_index + 1)
# calculate counts
counts = np.divide(sums, contents)
# shift hist data by half of the binwidth
binwidth_x = abs(edges[0][1] - edges[0][0])
bincenters_x = np.array(edges[0][:-1]) + binwidth_x / 2.
binwidth_y = abs(edges[1][1] - edges[1][0])
bincenters_y = np.array(edges[1][:-1]) + binwidth_y / 2.
# return counts (x, y)-array, x_edges and y_edges data
return contents, counts, bincenters_x, bincenters_y, edges[0], edges[
1], errors
def nua_raw(awesome, hist):
nuahist = awesome.FindObject(hist)
Zinit = hist2array(nuahist)
Zinit[Zinit == 0] = np.nan
return Zinit
def check_array2hist(hist):
shape = np.array([hist.GetNbinsX(), hist.GetNbinsY(), hist.GetNbinsZ()])
shape = shape[:hist.GetDimension()]
arr = RNG.randint(0, 10, size=shape)
rnp.array2hist(arr, hist)
arr_hist = rnp.hist2array(hist)
assert_array_equal(arr_hist, arr)
# Check behaviour if errors are supplied
errors = arr * 0.1
_hist = hist.Clone()
_hist.Reset()
rnp.array2hist(arr, _hist, errors=errors)
arr_hist = rnp.hist2array(_hist)
assert_array_equal(arr_hist, arr)
if hist.GetDimension() == 1:
errors_from_hist = np.array([_hist.GetBinError(ix)
for ix in range(1, _hist.GetNbinsX() + 1)])
if hist.GetDimension() == 2:
errors_from_hist = np.array([[_hist.GetBinError(ix, iy)
for iy in range(1, _hist.GetNbinsY() + 1)]
for ix in range(1, _hist.GetNbinsX() + 1)])
if hist.GetDimension() == 3:
errors_from_hist = np.array([[[_hist.GetBinError(ix, iy, iz)
for iz in range(1, _hist.GetNbinsZ() + 1)]
for iy in range(1, _hist.GetNbinsY() + 1)]
for ix in range(1, _hist.GetNbinsX() + 1)])
assert_array_equal(errors, errors_from_hist)
shape_overflow = shape + 2
arr_overflow = RNG.randint(0, 10, size=shape_overflow)
hist_overflow = hist.Clone()
hist_overflow.Reset()
rnp.array2hist(arr_overflow, hist_overflow)
arr_hist_overflow = rnp.hist2array(hist_overflow, include_overflow=True)
assert_array_equal(arr_hist_overflow, arr_overflow)
if len(shape) == 1:
return
# overflow not specified on all axes
arr_overflow2 = arr_overflow[1:-1]
hist_overflow2 = hist.Clone()
hist_overflow2.Reset()
rnp.array2hist(arr_overflow2, hist_overflow2)
arr_hist_overflow2 = rnp.hist2array(hist_overflow2, include_overflow=True)
assert_array_equal(arr_hist_overflow2[1:-1], arr_overflow2)
def __init__(self, working_points, functions, efficiency_map):
efficiency_array = hist2array(efficiency_map)
working_points_indices = find_closest(working_points, efficiency_array)
self.function_index_map = efficiency_map.empty_clone()
array2hist(working_points_indices, self.function_index_map)
self.indices = working_points_indices
self.functions = functions
self.dim = len(efficiency_array.shape)
def hist2d_to_matrix( hist2d ):
'''
hist2d to matrix + bin edges
'''
from root_numpy import hist2array
values = hist2array(hist2d)
xedges = list(hist2d.xedges())
yedges = list(hist2d.yedges())
return values, xedges, yedges
def get_hist(rfile, histname, get_overflow=False):
"""Read a 1D Histogram."""
import root_numpy as rnp
rfile = open_rfile(rfile)
hist = rfile[histname]
xlims = np.array(list(hist.xedges()))
bin_values = rnp.hist2array(hist, include_overflow=get_overflow)
rfile.close()
return bin_values, xlims
def check_hist2array(hist, include_overflow, copy):
array = rnp.hist2array(hist, include_overflow=include_overflow, copy=copy)
assert_equal(hist.GetDimension(), array.ndim)
for iaxis, axis in enumerate('XYZ'[:array.ndim]):
if include_overflow:
assert_equal(array.shape[iaxis],
getattr(hist, 'GetNbins{0}'.format(axis))() + 2)
else:
assert_equal(array.shape[iaxis],
getattr(hist, 'GetNbins{0}'.format(axis))())
# non-zero elements
assert_true(np.any(array))
def check_hist2array(hist, include_overflow, copy):
array = rnp.hist2array(hist, include_overflow=include_overflow, copy=copy)
assert_equal(hist.GetDimension(), array.ndim)
for iaxis, axis in enumerate('XYZ'[:array.ndim]):
if include_overflow:
assert_equal(array.shape[iaxis],
getattr(hist, 'GetNbins{0}'.format(axis))() + 2)
else:
assert_equal(array.shape[iaxis],
getattr(hist, 'GetNbins{0}'.format(axis))())
hist_sum = hist.Integral()
assert_true(hist_sum > 0)
assert_equal(hist_sum, np.sum(array))
def test_hist2array():
assert_raises(TypeError, rnp.hist2array, object())
for ndim in (1, 2, 3):
for hist_type in 'DFISC':
hist = make_histogram(hist_type, shape=(5,) * ndim)
yield check_hist2array, hist, False, False
yield check_hist2array, hist, False, True
yield check_hist2array, hist, True, False
yield check_hist2array, hist, True, True
yield check_hist2array_THn, hist
# check that the memory was copied
arr = rnp.hist2array(hist, copy=True)
hist_sum = hist.Integral()
assert_true(hist_sum > 0)
hist.Reset()
assert_equal(np.sum(arr), hist_sum)
# check that the memory is shared
hist = make_histogram(hist_type, shape=(5,) * ndim)
arr = rnp.hist2array(hist, copy=False)
hist_sum = hist.Integral()
assert_true(hist_sum > 0)
assert_true(np.sum(arr) == hist_sum)
hist.Reset()
assert_true(np.sum(arr) == 0)
def th2_to_arrays(th2):
# NOTE: man how much I hate ROOT!
# So much effort to do the simplest thing...
# Get first all the lower edges of the bins, then the last edge is the upper edge of the last bin
# (so these edges can be used in np.histogram)
n_x = th2.GetNbinsX()
xax = th2.GetXaxis()
x_edges = _get_edges(xax, n_x)
# Same for y
n_y = th2.GetNbinsY()
yax = th2.GetYaxis()
y_edges = _get_edges(yax, n_y)
# Finally get the array of values
matrix = root_numpy.hist2array(th2)
return x_edges, y_edges, matrix
def check_hist2array_edges(hist, ndim, bins):
_, edges = rnp.hist2array(hist, return_edges=True)
assert_equal(len(edges), ndim)
for axis_edges in edges:
assert_array_equal(axis_edges, np.arange(bins + 1, dtype=np.double))
if checkExtension( inFile, "root" ):
cOutputName = changeExtension( inFile, '.npz' )
if args.change_output_folder:
import os.path
cOutputName = os.path.join( os.path.abspath(args.change_output_folder) , os.path.basename(cOutputName) )
f = ROOT.TFile( inFile, 'r' )
data = {}
for keyName, obj in getall(f):
mainLogger.debug("Reading key: %s", keyName)
shortKey = keyName.split('/')[-1]
if not issubclass(type(obj), ROOT.TH1):
mainLogger.verbose("Ignoring key: %s", shortKey )
continue
hist = obj
if all( [wanted not in shortKey for wanted in args.filter_keys] ):
mainLogger.debug("key <%s> does not match any filter", shortKey )
continue
if all( [exclude in shortKey for exclude in args.exclude_keys] ):
mainLogger.debug("key <%s> matches exclude pattern", shortKey )
continue
if not hist:
mainLogger.warning("Couldn't retrieve histogram with key: %s", shortKey )
data[ shortKey ] = rnp.hist2array( hist, include_overflow=True, return_edges=True )
savedPath = save(data, cOutputName, protocol = 'savez_compressed')
mainLogger.info("Successfully created numpy file: %s", cOutputName)
else:
mainLogger.error("Cannot transform file '%s' to numpy format." % inFile)
# end of (for fileCollection)
for (ioff, off) in enumerate(offMC):
print off
for (izen, zen) in enumerate(zenMC):
print zen
filehistoarea = results.directory + "/" + results.config + "/gFixedEnergy_paris_0-8-8-8_CamOptimal_hwtrig_eff" + str(
eff) + "/CollectionArea.root"
filehistoresol = results.directory + "/" + results.config + "/gFixedEnergy_paris_0-8-8-8_CamOptimal_hwtrig_eff" + str(
eff) + "/EnergyResolution.root"
TFileArea = ROOT.TFile(filehistoarea)
TFileResol = ROOT.TFile(filehistoresol)
if (izen == 0):
name_hist_area = "EffArea_00deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
name_hist_biais = "Resol_Biais_00deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
name_hist_sigma = "Resol_Sigma_00deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
else:
name_hist_area = "EffArea_" + str(zen) + "deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
name_hist_biais = "Resol_Biais_" + str(zen) + "deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
name_hist_sigma = "Resol_Sigma_" + str(zen) + "deg_" + str(off) + "off_eff" + str(eff) + "_FixedE"
histoarea = TFileArea.Get(name_hist_area)
histobiais = TFileResol.Get(name_hist_biais)
histosigma = TFileResol.Get(name_hist_sigma)
AreaArray = hist2array(histoarea)[ind_area]
AreaBiais = hist2array(histobiais)[ind_resol]
AreaSigma = hist2array(histosigma)[ind_resol]
TableArea[:, ioff, izen, ieff] = AreaArray
TableBiais[:, ioff, izen, ieff] = AreaBiais
TableSigma[:, ioff, izen, ieff] = AreaSigma
outdir="output_4Dnumpyarrays"
np.savez(outdir+"/IRF_"+results.config+".npz", TableArea=TableArea, TableBiais=TableBiais, TableSigma=TableSigma, enMC=enMC, lnenMC=lnenMC,
zenMC=zenMC, offMC=offMC, effMC=effMC)