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() # nbins = -1 nprocesses = -1 nuisances = -1 binline = [] processline = [] sigline = [] for l in 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 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): 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 l in 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 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]) # check if there are bins with no rate for b in ret.bins: np_bin = sum([(ret.exp[b][p] != 0) for (b1, p, s) in ret.keyline if b1 == b]) ns_bin = sum([(ret.exp[b][p] != 0) for (b1, p, s) in ret.keyline if b1 == b and s == True]) nb_bin = sum([(ret.exp[b][p] != 0) for (b1, p, s) in ret.keyline if b1 == b and s != True]) if np_bin == 0: raise RuntimeError, "Bin %s has no processes contributing to it" % b if ns_bin == 0 and not options.allowNoSignal: stderr.write( "Warning: Bin %s has no signal processes contributing to it\n" % b) if nb_bin == 0 and not options.allowNoBackground: raise RuntimeError, "Bin %s has no background processes contributing to it" % b # cleanup systematics that have no effect to avoid zero derivatives syst2 = [] for lsyst, nofloat, pdf, args, errline in ret.systs: nonNullEntries = 0 if pdf == "param": # this doesn't have an errline syst2.append((lsyst, nofloat, pdf, args, errline)) continue for (b, p, s) in ret.keyline: r = errline[b][p] nullEffect = (r == 0.0 or (pdf == "lnN" and r == 1.0)) if not nullEffect and ret.exp[b][p] != 0: nonNullEntries += 1 # is this a zero background? if nonNullEntries != 0: syst2.append((lsyst, nofloat, pdf, args, errline)) elif nuisances != -1: nuisances -= 1 # remove from count of nuisances, since qe skipped it ret.systs = syst2 # remove them if options.stat asks so if options.stat: nuisances = 0 ret.systs = [] # check number of nuisances if nuisances == -1: nuisances = len(ret.systs) elif len(ret.systs) != nuisances: raise RuntimeError, "Found %d systematics, expected %d" % (len( ret.systs), nuisances) # set boolean to know about shape ret.hasShapes = (len(ret.shapeMap) > 0) # return result return ret
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() # nbins = -1; nprocesses = -1; nuisances = -1; binline = []; processline = []; sigline = [] for l in 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 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): 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 l in 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 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]) # check if there are bins with no rate for b in ret.bins: np_bin = sum([(ret.exp[b][p] != 0) for (b1,p,s) in ret.keyline if b1 == b]) ns_bin = sum([(ret.exp[b][p] != 0) for (b1,p,s) in ret.keyline if b1 == b and s == True]) nb_bin = sum([(ret.exp[b][p] != 0) for (b1,p,s) in ret.keyline if b1 == b and s != True]) if np_bin == 0: raise RuntimeError, "Bin %s has no processes contributing to it" % b if ns_bin == 0 and not options.allowNoSignal: stderr.write("Warning: Bin %s has no signal processes contributing to it\n" % b) if nb_bin == 0 and not options.allowNoBackground: raise RuntimeError, "Bin %s has no background processes contributing to it" % b # cleanup systematics that have no effect to avoid zero derivatives syst2 = [] for lsyst,nofloat,pdf,args,errline in ret.systs: nonNullEntries = 0 if pdf == "param": # this doesn't have an errline syst2.append((lsyst,nofloat,pdf,args,errline)) continue for (b,p,s) in ret.keyline: r = errline[b][p] nullEffect = (r == 0.0 or (pdf == "lnN" and r == 1.0)) if not nullEffect and ret.exp[b][p] != 0: nonNullEntries += 1 # is this a zero background? if nonNullEntries != 0: syst2.append((lsyst,nofloat,pdf,args,errline)) elif nuisances != -1: nuisances -= 1 # remove from count of nuisances, since qe skipped it ret.systs = syst2 # remove them if options.stat asks so if options.stat: nuisances = 0 ret.systs = [] # check number of nuisances if nuisances == -1: nuisances = len(ret.systs) elif len(ret.systs) != nuisances: raise RuntimeError, "Found %d systematics, expected %d" % (len(ret.systs), nuisances) # set boolean to know about shape ret.hasShapes = (len(ret.shapeMap) > 0) # return result return ret