def parseCard(file, options):
if type(file) == type("str"):
raise RuntimeError, "You should pass as argument to parseCards a file object, stream or a list of lines, not a string"
ret = Datacard()
# resetting these here to defaults, parseCard will fill them up
ret.discretes = []
ret.groups = {}
#
nbins = -1
nprocesses = -1
nuisances = -1
binline = []
processline = []
sigline = []
shapesUseBin = False
lineNumber = None
try:
getattr(options, "evaluateEdits")
except:
setattr(options, "evaluateEdits", True)
try:
for lineNumber, l in enumerate(file):
f = l.split()
if len(f) < 1: continue
if f[0] == "imax":
nbins = int(f[1]) if f[1] != "*" else -1
if f[0] == "jmax":
nprocesses = int(f[1]) + 1 if f[1] != "*" else -1
if f[0] == "kmax":
nuisances = int(f[1]) if f[1] != "*" else -1
if f[0] == "shapes":
if not options.bin:
raise RuntimeError, "Can use shapes only with binary output mode"
if len(f) < 4: raise RuntimeError, "Malformed shapes line"
if not ret.shapeMap.has_key(f[2]): ret.shapeMap[f[2]] = {}
if ret.shapeMap[f[2]].has_key(f[1]):
raise RuntimeError, "Duplicate definition for process '%s', channel '%s'" % (
f[1], f[2])
ret.shapeMap[f[2]][f[1]] = f[3:]
if "$CHANNEL" in l: shapesUseBin = True
if f[2] != "*": shapesUseBin = True
if f[0] == "Observation" or f[0] == "observation":
ret.obs = [float(x) for x in f[1:]]
if nbins == -1: nbins = len(ret.obs)
if len(ret.obs) != nbins:
raise RuntimeError, "Found %d observations but %d bins have been declared" % (
len(ret.obs), nbins)
if binline != []:
if len(binline) != len(ret.obs):
raise RuntimeError, "Found %d bins (%s) but %d bins have been declared" % (
len(ret.bins), ret.bins, nbins)
ret.bins = binline
ret.obs = dict([(b, ret.obs[i])
for i, b in enumerate(ret.bins)])
binline = []
if f[0] == "bin":
binline = []
for b in f[1:]:
if re.match("[0-9]+", b):
raise RuntimeError, "Error: Bin %(b)s starts with a digit!" % locals(
)
binline.append(b)
if f[0] == "process":
if processline == []: # first line contains names
processline = f[1:]
if len(binline) != len(processline):
raise RuntimeError, "'bin' line has a different length than 'process' line."
continue
sigline = f[1:] # second line contains ids
if re.match("-?[0-9]+", processline[0]) and not re.match(
"-?[0-9]+", sigline[0]):
(processline, sigline) = (sigline, processline)
if len(sigline) != len(processline):
raise RuntimeError, "'bin' line has a different length than 'process' line."
hadBins = (len(ret.bins) > 0)
for i, b in enumerate(binline):
p = processline[i]
s = (int(sigline[i]) <= 0
) # <=0 for signals, >0 for backgrounds
ret.keyline.append((b, processline[i], s))
if hadBins:
if b not in ret.bins:
raise RuntimeError, "Bin %s not among the declared bins %s" % (
b, ret.bins)
else:
if b not in ret.bins: ret.bins.append(b)
if p not in ret.processes: ret.processes.append(p)
if nprocesses == -1: nprocesses = len(ret.processes)
if nbins == -1: nbins = len(ret.bins)
if not options.noJMax:
if nprocesses != len(ret.processes):
raise RuntimeError, "Found %d processes (%s), declared jmax = %d" % (
len(ret.processes), ret.processes, nprocesses)
if nbins != len(ret.bins):
raise RuntimeError, "Found %d bins (%s), declared imax = %d" % (
len(ret.bins), ret.bins, nbins)
ret.exp = dict([(b, {}) for b in ret.bins])
ret.isSignal = dict([(p, None) for p in ret.processes])
if ret.obs != [] and type(
ret.obs
) == list: # still as list, must change into map with bin names
ret.obs = dict([(b, ret.obs[i])
for i, b in enumerate(ret.bins)])
for (b, p, s) in ret.keyline:
if ret.isSignal[p] == None:
ret.isSignal[p] = s
elif ret.isSignal[p] != s:
raise RuntimeError, "Process %s is declared as signal in some bin and as background in some other bin" % p
ret.signals = [p for p, s in ret.isSignal.items() if s == True]
if len(ret.signals) == 0 and not options.allowNoSignal:
raise RuntimeError, "You must have at least one signal process (id <= 0)"
if f[0] == "rate":
if processline == []:
raise RuntimeError, "Missing line with process names before rate line"
if sigline == []:
raise RuntimeError, "Missing line with process id before rate line"
if len(f[1:]) != len(ret.keyline):
raise RuntimeError, "Malformed rate line: length %d, while bins and process lines have length %d" % (
len(f[1:]), len(ret.keyline))
for (b, p, s), r in zip(ret.keyline, f[1:]):
ret.exp[b][p] = float(r)
break # rate is the last line before nuisances
# parse nuisances
for lineNumber, l in enumerate(file):
if l.startswith("--"): continue
l = re.sub("\\s*#.*", "", l)
l = re.sub("(?<=\\s)-+(\\s|$)", " 0\\1", l)
f = l.split()
if len(f) <= 1: continue
nofloat = False
lsyst = f[0]
pdf = f[1]
args = []
numbers = f[2:]
if lsyst.endswith("[nofloat]"):
lsyst = lsyst.replace("[nofloat]", "")
nofloat = True
if options.nuisancesToExclude and isVetoed(
lsyst, options.nuisancesToExclude):
if options.verbose > 0:
stderr.write(
"Excluding nuisance %s selected by a veto pattern among %s\n"
% (lsyst, options.nuisancesToExclude))
if nuisances != -1: nuisances -= 1
continue
if re.match("[0-9]+", lsyst): lsyst = "theta" + lsyst
if pdf == "lnN" or pdf == "lnU" or pdf == "gmM" or pdf == "trG" or pdf.startswith(
"shape"):
pass # nothing special to do
elif pdf == "gmN":
args = [int(f[2])]
numbers = f[3:]
elif pdf == "unif":
args = [float(f[2]), float(f[3])]
numbers = f[4:]
elif pdf == "dFD" or pdf == "dFD2":
args = [float(f[2])]
numbers = f[3:]
elif pdf == "constr":
args = f[2:]
ret.systs.append([lsyst, nofloat, pdf, args, []])
continue
elif pdf == "param":
# for parametric uncertainties, there's no line to account per bin/process effects
# just assume everything else is an argument and move on
args = f[2:]
if len(args) <= 1:
raise RuntimeError, "Uncertainties of type 'param' must have at least two arguments (mean and sigma)"
ret.systs.append([lsyst, nofloat, pdf, args, []])
continue
elif pdf == "flatParam":
ret.flatParamNuisances[lsyst] = True
#for flat parametric uncertainties, code already does the right thing as long as they are non-constant RooRealVars linked to the model
continue
elif pdf == "extArg":
# look for additional parameters in workspaces
ret.extArgs[lsyst] = f[:]
continue
elif pdf == "rateParam":
if ("*" in f[3]) or ("*" in f[2]): # all channels/processes
found = False
for c in ret.processes:
for b in ret.bins:
if (not fnmatch.fnmatch(c, f[3])): continue
if (not fnmatch.fnmatch(b, f[2])): continue
f_tmp = f[:]
f_tmp[2] = b
f_tmp[3] = c
addRateParam(lsyst, f_tmp, ret)
found = True
if not found:
raise RuntimeError, "rateParam %s with process %r bin %r doesn't match anything." % (
lsyst, f[3], f[2])
else:
addRateParam(lsyst, f, ret)
continue
elif pdf == "discrete":
args = f[2:]
ret.discretes.append(lsyst)
continue
elif pdf == "edit":
if nuisances != -1: nuisances = -1
if options.evaluateEdits:
if options.verbose > 1:
print "Before edit: \n\t%s\n" % ("\n\t".join(
[str(x) for x in ret.systs]))
if options.verbose > 1:
print "Edit command: %s\n" % numbers
doEditNuisance(ret, numbers[0], numbers[1:])
if options.verbose > 1:
print "After edit: \n\t%s\n" % ("\n\t".join(
[str(x) for x in ret.systs]))
else:
if numbers[0] in ["changepdf", "freeze"]:
ret.nuisanceEditLines.append([numbers[0], numbers[1:]])
else:
ret.nuisanceEditLines.append(
[numbers[0], numbers[1], numbers[2], numbers[3:]])
continue
elif pdf == "group":
# This is not really a pdf type, but a way to be able to name groups of nuisances together
groupName = lsyst
groupNuisances = numbers
if not groupNuisances:
raise RuntimeError, "Syntax error for group '%s': empty line after 'group'." % groupName
defToks = ('=', '+=')
defTok = groupNuisances.pop(0)
if defTok not in defToks:
raise RuntimeError, "Syntax error for group '%s': first thing after 'group' is not '[+]=' but '%s'." % (
groupName, defTok)
if groupName not in ret.groups:
if defTok == '=':
ret.groups[groupName] = set(groupNuisances)
else:
raise RuntimeError, "Cannot append to group '%s' as it was not yet defined." % groupName
else:
if defTok == '+=':
ret.groups[groupName].update(set(groupNuisances))
else:
raise RuntimeError, "Will not redefine group '%s'. It previously contained '%s' and you now wanted it to contain '%s'." % (
groupName, ret.groups[groupName], groupNuisances)
continue
elif pdf == "autoMCStats":
if len(f) > 5:
raise RuntimeError, "Syntax for autoMCStats should be 'channel autoMCStats threshold [include-signal = 0] [hist-mode = 0]"
statThreshold = float(f[2])
statIncludeSig = bool(int(f[3])) if len(f) >= 4 else False
statHistMode = int(f[4]) if len(f) >= 5 else 1
statFlags = (statThreshold, statIncludeSig, statHistMode)
if "*" in lsyst:
for b in ret.bins:
if (not fnmatch.fnmatch(b, lsyst)): continue
ret.binParFlags[b] = statFlags
else:
if lsyst not in ret.bins:
raise RuntimeError, " No such channel '%s', malformed line:\n %s" % (
lsyst, ' '.join(f))
ret.binParFlags[lsyst] = statFlags
continue
else:
raise RuntimeError, "Unsupported pdf %s" % pdf
if len(numbers) < len(ret.keyline):
raise RuntimeError, "Malformed systematics line %s of length %d: while bins and process lines have length %d" % (
lsyst, len(numbers), len(ret.keyline))
errline = dict([(b, {}) for b in ret.bins])
nonNullEntries = 0
for (b, p, s), r in zip(ret.keyline, numbers):
if "/" in r: # "number/number"
if (pdf not in ["lnN", "lnU"]) and ("?" not in pdf):
raise RuntimeError, "Asymmetric errors are allowed only for Log-normals"
errline[b][p] = [float(x) for x in r.split("/")]
for v in errline[b][p]:
if v <= 0.00:
raise ValueError(
'Found "%s" in the nuisances affecting %s for %s. This would lead to NANs later on, so please fix it.'
% (r, p, b))
else:
errline[b][p] = float(r)
#values of 0.0 are treated as 1.0; scrap negative values.
if pdf not in ["trG", "dFD", "dFD2"] and errline[b][p] < 0:
raise ValueError(
'Found "%s" in the nuisances affecting %s in %s. This would lead to NANs later on, so please fix it.'
% (r, p, b))
# set the rate to epsilon for backgrounds with zero observed sideband events.
if pdf == "gmN" and ret.exp[b][p] == 0 and float(r) != 0:
ret.exp[b][p] = 1e-6
ret.systs.append([lsyst, nofloat, pdf, args, errline])
except Exception, ex:
if lineNumber != None:
msg = "Error reading line %d" % (lineNumber + 1)
if hasattr(file, 'name'):
msg += " of file " + file.name
msg += ": " + ex.args[0]
ex.args = (msg, ) + ex.args[1:]
raise
def parseCard(file, options):
if type(file) == type("str"):
raise RuntimeError, "You should pass as argument to parseCards a file object, stream or a list of lines, not a string"
ret = Datacard()
ret.discretes=[]
ret.groups={}
#
nbins = -1;
nprocesses = -1;
nuisances = -1;
binline = []; processline = []; sigline = []
shapesUseBin = False
lineNumber = None
try:
for lineNumber,l in enumerate(file):
f = l.split();
if len(f) < 1: continue
if f[0] == "imax":
nbins = int(f[1]) if f[1] != "*" else -1
if f[0] == "jmax":
nprocesses = int(f[1])+1 if f[1] != "*" else -1
if f[0] == "kmax":
nuisances = int(f[1]) if f[1] != "*" else -1
if f[0] == "shapes":
if not options.bin: raise RuntimeError, "Can use shapes only with binary output mode"
if len(f) < 4: raise RuntimeError, "Malformed shapes line"
if not ret.shapeMap.has_key(f[2]): ret.shapeMap[f[2]] = {}
if ret.shapeMap[f[2]].has_key(f[1]): raise RuntimeError, "Duplicate definition for process '%s', channel '%s'" % (f[1], f[2])
ret.shapeMap[f[2]][f[1]] = f[3:]
if "$CHANNEL" in l: shapesUseBin = True
if f[2] != "*": shapesUseBin = True
if f[0] == "Observation" or f[0] == "observation":
ret.obs = [ float(x) for x in f[1:] ]
if nbins == -1: nbins = len(ret.obs)
if len(ret.obs) != nbins: raise RuntimeError, "Found %d observations but %d bins have been declared" % (len(ret.obs), nbins)
if binline != []:
if len(binline) != len(ret.obs): raise RuntimeError, "Found %d bins (%s) but %d bins have been declared" % (len(ret.bins), ret.bins, nbins)
ret.bins = binline
ret.obs = dict([(b,ret.obs[i]) for i,b in enumerate(ret.bins)])
binline = []
if f[0] == "bin":
binline = []
for b in f[1:]:
if re.match("[0-9]+", b):
if shapesUseBin: stderr.write("Warning: Bin %(b)s starts with a digit. Will call it 'bin%(b)s' but this may break shapes.\n" % locals())
b = "bin"+b
# TODO Here should be some patching of the shapes names in order to not get errors later.
binline.append(b)
if f[0] == "process":
if processline == []: # first line contains names
processline = f[1:]
if len(binline) != len(processline): raise RuntimeError, "'bin' line has a different length than 'process' line."
continue
sigline = f[1:] # second line contains ids
if re.match("-?[0-9]+", processline[0]) and not re.match("-?[0-9]+", sigline[0]):
(processline,sigline) = (sigline,processline)
if len(sigline) != len(processline): raise RuntimeError, "'bin' line has a different length than 'process' line."
hadBins = (len(ret.bins) > 0)
for i,b in enumerate(binline):
p = processline[i];
s = (int(sigline[i]) <= 0) # <=0 for signals, >0 for backgrounds
ret.keyline.append((b, processline[i], s))
if hadBins:
if b not in ret.bins: raise RuntimeError, "Bin %s not among the declared bins %s" % (b, ret.bins)
else:
if b not in ret.bins: ret.bins.append(b)
if p not in ret.processes: ret.processes.append(p)
if nprocesses == -1: nprocesses = len(ret.processes)
if nbins == -1: nbins = len(ret.bins)
if not options.noJMax:
if nprocesses != len(ret.processes): raise RuntimeError, "Found %d processes (%s), declared jmax = %d" % (len(ret.processes),ret.processes,nprocesses)
if nbins != len(ret.bins): raise RuntimeError, "Found %d bins (%s), declared imax = %d" % (len(ret.bins),ret.bins,nbins)
ret.exp = dict([(b,{}) for b in ret.bins])
ret.isSignal = dict([(p,None) for p in ret.processes])
if ret.obs != [] and type(ret.obs) == list: # still as list, must change into map with bin names
ret.obs = dict([(b,ret.obs[i]) for i,b in enumerate(ret.bins)])
for (b,p,s) in ret.keyline:
if ret.isSignal[p] == None:
ret.isSignal[p] = s
elif ret.isSignal[p] != s:
raise RuntimeError, "Process %s is declared as signal in some bin and as background in some other bin" % p
ret.signals = [p for p,s in ret.isSignal.items() if s == True]
if len(ret.signals) == 0 and not options.allowNoSignal: raise RuntimeError, "You must have at least one signal process (id <= 0)"
if f[0] == "rate":
if processline == []: raise RuntimeError, "Missing line with process names before rate line"
if sigline == []: raise RuntimeError, "Missing line with process id before rate line"
if len(f[1:]) != len(ret.keyline): raise RuntimeError, "Malformed rate line: length %d, while bins and process lines have length %d" % (len(f[1:]), len(ret.keyline))
for (b,p,s),r in zip(ret.keyline,f[1:]):
ret.exp[b][p] = float(r)
break # rate is the last line before nuisances
# parse nuisances
for lineNumber,l in enumerate(file):
if l.startswith("--"): continue
l = re.sub("\\s*#.*","",l)
l = re.sub("(?<=\\s)-+(\\s|$)"," 0\\1",l);
f = l.split();
if len(f) <= 1: continue
nofloat = False
lsyst = f[0]; pdf = f[1]; args = []; numbers = f[2:];
if lsyst.endswith("[nofloat]"):
lsyst = lsyst.replace("[nofloat]","")
nofloat = True
if options.nuisancesToExclude and isVetoed(lsyst, options.nuisancesToExclude):
if options.verbose > 0: stderr.write("Excluding nuisance %s selected by a veto pattern among %s\n" % (lsyst, options.nuisancesToExclude))
if nuisances != -1: nuisances -= 1
continue
if re.match("[0-9]+",lsyst): lsyst = "theta"+lsyst
if pdf == "lnN" or pdf == "lnU" or pdf == "gmM" or pdf == "trG" or pdf.startswith("shape"):
pass # nothing special to do
elif pdf == "gmN":
args = [int(f[2])]; numbers = f[3:];
elif pdf == "unif":
args = [float(f[2]), float(f[3])]; numbers = f[4:];
elif pdf == "dFD" or pdf == "dFD2":
args = [float(f[2])]; numbers = f[3:];
elif pdf == "param":
# for parametric uncertainties, there's no line to account per bin/process effects
# just assume everything else is an argument and move on
args = f[2:]
if len(args) <= 1: raise RuntimeError, "Uncertainties of type 'param' must have at least two arguments (mean and sigma)"
ret.systs.append([lsyst,nofloat,pdf,args,[]])
continue
elif pdf == "flatParam":
ret.flatParamNuisances[lsyst] = True
#for flat parametric uncertainties, code already does the right thing as long as they are non-constant RooRealVars linked to the model
continue
elif pdf=="discrete":
args = f[2:]
ret.discretes.append(lsyst)
continue
elif pdf=="edit":
if nuisances != -1: nuisances = -1
if options.verbose > 1: print "Before edit: \n\t%s\n" % ("\n\t".join( [str(x) for x in ret.systs] ))
if options.verbose > 1: print "Edit command: %s\n" % numbers
doEditNuisance(ret, numbers[0], numbers[1:])
if options.verbose > 1: print "After edit: \n\t%s\n" % ("\n\t".join( [str(x) for x in ret.systs] ))
continue
elif pdf=="group":
# This is not really a pdf type, but a way to be able to name groups of nuisances together
groupName = lsyst
groupNuisances = numbers
if not groupNuisances:
raise RuntimeError, "Syntax error for group '%s': empty line after 'group'." % groupName
defToks = ('=','+=')
defTok = groupNuisances.pop(0)
if defTok not in defToks:
raise RuntimeError, "Syntax error for group '%s': first thing after 'group' is not '[+]=' but '%s'." % (groupName,defTok)
if groupName not in ret.groups:
if defTok=='=':
ret.groups[groupName] = set(groupNuisances)
else:
raise RuntimeError, "Cannot append to group '%s' as it was not yet defined." % groupName
else:
if defTok=='+=' :
ret.groups[groupName].update( set(groupNuisances) )
else:
raise RuntimeError, "Will not redefine group '%s'. It previously contained '%s' and you now wanted it to contain '%s'." % (groupName,ret.groups[groupName],groupNuisances)
continue
else:
raise RuntimeError, "Unsupported pdf %s" % pdf
if len(numbers) < len(ret.keyline): raise RuntimeError, "Malformed systematics line %s of length %d: while bins and process lines have length %d" % (lsyst, len(numbers), len(ret.keyline))
errline = dict([(b,{}) for b in ret.bins])
nonNullEntries = 0
for (b,p,s),r in zip(ret.keyline,numbers):
if "/" in r: # "number/number"
if (pdf not in ["lnN","lnU"]) and ("?" not in pdf): raise RuntimeError, "Asymmetric errors are allowed only for Log-normals"
errline[b][p] = [ float(x) for x in r.split("/") ]
for v in errline[b][p]:
if v <= 0.00: raise ValueError('Found "%s" in the nuisances affecting %s for %s. This would lead to NANs later on, so please fix it.'%(r,p,b))
else:
errline[b][p] = float(r)
#values of 0.0 are treated as 1.0; scrap negative values.
if pdf not in ["trG", "dFD", "dFD2"] and errline[b][p] < 0: raise ValueError('Found "%s" in the nuisances affecting %s in %s. This would lead to NANs later on, so please fix it.'%(r,p,b))
# set the rate to epsilon for backgrounds with zero observed sideband events.
if pdf == "gmN" and ret.exp[b][p] == 0 and float(r) != 0: ret.exp[b][p] = 1e-6
ret.systs.append([lsyst,nofloat,pdf,args,errline])
except Exception, ex:
if lineNumber != None:
msg = "Error reading line %d" % (lineNumber + 1)
if hasattr(file,'name'):
msg += " of file " + file.name
msg += ": " + ex.args[0]
ex.args = (msg, ) + ex.args[1:]
raise