def makeStartFromExplore(ListOfChains,StablePerc,SampleParamFile,OutputParamFile):
"""
Reads a list of single parameter step-exoploration chains
and prints a startparam file based on this data.
This routine also prints whether a chain has stabilized
the correct single-parameter acceptance rate.
"""
ListFiles = open(ListOfChains,'r')
ListFiles = ListFiles.readlines()
ModelParams = ReadStartParams(SampleParamFile)
step = {}
for file in ListFiles:
data = readMCMC(file.strip('\n'))
if data['acr'][-1] > 0.44-StablePerc and data['acr'][-1] < 0.44+StablePerc:
for par in data.keys():
if not isNonParam(par):
medfrac = np.median(data['frac'][-1000:])
print par+' has stabilized, acr = '+format(data['acr'][-1],'.2f')+' frac = '+str(medfrac)
step[par] = {'frac':medfrac}
else:
for par in data.keys():
if not isNonParam(par):
print par+' has NOT stabilized, acr = '+format(data['acr'][-1],'.2f')
for par in step.keys():
for key in ModelParams.keys():
if key == par:
ModelParams[par]['step'] = ModelParams[par]['step']*step[par]['frac']
ModelParams[par]['open'] = True
PrintModelParams(ModelParams,OutputParamFile)
def printDerivedParFile_MTQ_2011(ParFile,OutParFile):
"""
print the derived parameters in the format of the parameter file
"""
ModelParams = ReadStartParams(ParFile)
derived = {}
Period = computePeriod(ModelParams)
derived['Period'] = {'value':Period,'printformat':'.9f','open':True,'step':0.0}
RefFilt = ModelParams['RefFilt']['printformat']
# get Filter and Transit time tags
Tags = getTags(ModelParams)
# compute parameters used to compute lightcurve using the reference filter
Dref, v1ref, v2ref = MTQ_2011.MTQ_FilterParams(RefFilt,Tags,ModelParams)
u1ref, u2ref = LDC_v2u(v1ref,v2ref)
tT = ModelParams['tT']['value']
tG = ModelParams['tG']['value']
TransitRef = MTQ_2011.MTQ_getDerivedParams(Dref,tT,tG,u1ref,u2ref,Period)
#print TransitRef
derived['inc'] = {'value':TransitRef['inc']*180e0/np.pi,'printformat':'.4f','open':True,'step':0.0}
derived['b'] = {'value':TransitRef['b'],'printformat':'.6f','open':True,'step':0.0}
derived['aRs'] = {'value':TransitRef['aRs'],'printformat':'.6f','open':True,'step':0.0}
derived['velRs'] = {'value':TransitRef['velRs'],'printformat':'.6f','open':True,'step':0.0}
derived['rho_star'] = {'value':TransitRef['rho_star'],'printformat':'.6f','open':True,'step':0.0}
derived['RpRs'+'.'+ModelParams['RefFilt']['printformat']] = \
{'value':TransitRef['RpRs'],'printformat':'.9f','open':True,'step':0.0}
for key in ModelParams.keys():
if key.startswith('T0'):
split_TT = map(str,key.split('.'))
transit_tag = split_TT[1].strip()
# compute D, v1, v2 and then u1 and u2 for a given transit tag
D, v1, v2 = MTQ_2011.MTQ_FilterParams(transit_tag,Tags,ModelParams)
u1, u2 = LDC_v2u(v1,v2)
RpRs = computeRpRs(u1,u2,tT,tG,D)
filterD = filterMatchD(transit_tag,Tags,ModelParams)
#print filterD
derived['RpRs'+'.'+filterD] = {'value':RpRs,'printformat':'.9f','open':True,'step':0.0}
PrintModelParams(derived,OutParFile)
def MinuitPar2Err(ParFile,ErrFile):
""" Convert a Minuit par file to an error file """
ModelParams = ReadStartParams(ParFile)
OutFile = open(ErrFile,'w')
header = '# parname | value | lower | upper | useSingle ?'
print >> OutFile, header
for par in ModelParams.keys():
if par.lower() != 'reffilt':
if ModelParams[par]['open']:
ValString = format(ModelParams[par]['value'],ModelParams[par]['printformat'])
ErrString = format(ModelParams[par]['step'],ModelParams[par]['printformat'])
print >> OutFile, par+'|'+ValString+'|'+ErrString+'|'+ErrString+'| True '
else:
ValString = format(ModelParams[par]['value'],ModelParams[par]['printformat'])
ErrString = 'nan'
print >> OutFile, par+'|'+ValString+'|'+ErrString+'|'+ErrString+'| False '
OutFile.close()
def printErrors(MCMCfile,BestfitFile,OutputFile):
""" Gets data out from the MCMC data file and the BESTFIT parameters file and prints uncertainties """
mcmcData = readMCMC(MCMCfile)
BestFitParams = ReadStartParams(BestfitFile)
erf15 = ((1e0 - scipy.special.erf(1e0/np.sqrt(2e0)))/2e0)
erf84 = (1e0 - erf15)
OutFileObject = open(OutputFile,'w')
print >> OutFileObject, '# Parameter | low15 | upp84 | use Single ?'
for param in BestFitParams.keys():
if BestFitParams[param]['open']:
sort_list = sorted(mcmcData[param])
Npoints = len(mcmcData[param])
id84 = long(round(erf84*(Npoints-1)))
id15 = long(round(erf15*(Npoints-1)))
low15 = abs(BestFitParams[param]['value']-sort_list[id15])
upp84 = abs(BestFitParams[param]['value']-sort_list[id84])
if low15 >= upp84:
greater = low15
lower = upp84
else:
greater = upp84
lower = low15
useSingle = False
if 1.1*lower >= 0.9*greater:
useSingle = True
print >> OutFileObject, param+'|'+\
format(BestFitParams[param]['value'],BestFitParams[param]['printformat'])+'|'+\
format(low15,BestFitParams[param]['printformat'])+'|'+\
format(upp84,BestFitParams[param]['printformat'])+'|'+\
str(useSingle)+'|:'
else:
if param.lower() != 'reffilt':
print >> OutFileObject, param+'|'+\
format(BestFitParams[param]['value'],BestFitParams[param]['printformat'])+'|'+\
format(float('nan'),BestFitParams[param]['printformat'])+'|'+\
format(float('nan'),BestFitParams[param]['printformat'])+'|'+\
str(True)+'|:'
OutFileObject.close()
def printDerived_MTQ_2011(STARTFILE,MCMCfile,DerivedFile):
""" print a file with Derived parameters from the MCMC ensemble. """
hdrKeys = readMCMChdr(MCMCfile)
ModelParams = ReadStartParams(STARTFILE)
mcmcFile = open(MCMCfile,'r')
mcmcFile = mcmcFile.readlines()
OutFileObject = open(DerivedFile,'w')
for line in mcmcFile:
derived = {}
if not line.startswith('#'):
data_line = ReadMCMCline(line,hdrKeys)
print 'step/line = ',format(long(data_line['istep']),'n')
for key in ModelParams.keys():
if ModelParams[key]['open']:
ModelParams[key]['value'] = data_line[key]
Period = computePeriod(ModelParams)
derived['Period'] = {'value':Period,'printformat':'.9f'}
RefFilt = ModelParams['RefFilt']['printformat']
# get Filter and Transit time tags
Tags = getTags(ModelParams)
# compute parameters used to compute lightcurve using the reference filter
Dref, v1ref, v2ref = MTQ_2011.MTQ_FilterParams(RefFilt,Tags,ModelParams)
u1ref, u2ref = LDC_v2u(v1ref,v2ref)
tT = ModelParams['tT']['value']
tG = ModelParams['tG']['value']
TransitRef = MTQ_2011.MTQ_getDerivedParams(Dref,tT,tG,u1ref,u2ref,Period)
#print TransitRef
derived['inc'] = {'value':TransitRef['inc']*180e0/np.pi,'printformat':'.4f'}
derived['b'] = {'value':TransitRef['b'],'printformat':'.6f'}
derived['aRs'] = {'value':TransitRef['aRs'],'printformat':'.6f'}
derived['velRs'] = {'value':TransitRef['velRs'],'printformat':'.6f'}
derived['rho_star'] = {'value':TransitRef['rho_star'],'printformat':'.6f'}
derived['RpRs'+'.'+ModelParams['RefFilt']['printformat']] = \
{'value':TransitRef['RpRs'],'printformat':'.9f'}
for key in ModelParams.keys():
if key.startswith('T0'):
split_TT = map(str,key.split('.'))
transit_tag = split_TT[1].strip()
# compute D, v1, v2 and then u1 and u2 for a given transit tag
D, v1, v2 = MTQ_2011.MTQ_FilterParams(transit_tag,Tags,ModelParams)
u1, u2 = LDC_v2u(v1,v2)
RpRs = computeRpRs(u1,u2,tT,tG,D)
filterD = filterMatchD(transit_tag,Tags,ModelParams)
#print filterD
derived['RpRs'+'.'+filterD] = {'value':RpRs,'printformat':'.9f'}
DerivedLine = ''
keylist = derived.keys()
Nkeys = len(keylist)
if data_line['istep'] == 0:
keyorder = {}
for i in range(len(keylist)):
keyorder[i] = keylist[i]
for i in range(Nkeys):
if i == 0:
DerivedLine =\
str(format(derived[keylist[i]]['value'],\
derived[keylist[i]]['printformat']))
else:
DerivedLine =\
DerivedLine+'|'+str(format(derived[keylist[i]]['value'],\
derived[keylist[i]]['printformat']))
else:
for i in range(Nkeys):
if i == 0:
DerivedLine =\
str(format(derived[keylist[i]]['value'],\
derived[keylist[i]]['printformat']))
else:
DerivedLine = DerivedLine+'|'+str(format(derived[keylist[i]]['value'],\
derived[keylist[i]]['printformat']))
DerivedLine = DerivedLine+'|'+str(format(data_line['istep'],'.0f'))+'|:'
print >> OutFileObject, DerivedLine
keyline = ''
for i in range(Nkeys):
if i == 0:
keyline = '#'+keylist[i]
else:
keyline = keyline+'|'+keylist[i]
keyline = keyline+'|istep|:'
OutFileObject.close()
#print >> OutFileObject, keyline
opencopy = open(DerivedFile,'r')
opencopy = opencopy.readlines()
os.system('rm -v %s' % (DerivedFile))
rearranged = open(DerivedFile,'w')
print >> rearranged, keyline
for iline in range(len(opencopy)):
print >> rearranged, opencopy[iline].strip('\n')
rearranged.close()