def randomrun(LogLikelihood,Prior,n_dims,n_params,n_live_points,n_print,outputfiles_basename,outputfiles_filename):
f_out = open(os.path.join(outputfiles_basename,outputfiles_filename),'w')
cube = []
for i in range(n_params): cube.append(0.0)
# Initialise the cube
sf.Info('Begin random scan ...')
Naccept = 0
for Nrun in range(n_live_points) :
for j in range(n_dims):
cube[j] = random()
Prior(cube, n_dims, n_params)
loglike = LogLikelihood(cube, n_dims, n_params)
if loglike > sf.log_zero:
Naccept += 1
f_out.write('\t'.join([str(x) for x in cube])+'\t'+str(loglike)+'\n')
f_out.flush()
if (Nrun+1)%n_print == 0:
print '------------ Num: %i ------------'%(Nrun+1)
print 'Input par = '+str(cube[0:n_dims])
print 'Output par = '+str(cube[n_dims:n_params])
print ' loglike = '+str(loglike)
print 'Accepted Num = '+str(Naccept)
print 'Total Num = '+str(Nrun+1)
def gridrun(LogLikelihood,Prior,n_dims,n_params,inpar,bin_num,n_print,outputfiles_basename,outputfiles_filename):
f_out = open(os.path.join(outputfiles_basename,outputfiles_filename),'w')
print "llllllllllllllllllllllllllllllllllllllllllllllllllllllllll"
print outputfiles_basename
print outputfiles_filename
print "n_dims", n_dims
print "n_params", n_params
ntotal = 1
cube = []
interval = {}
for i,name in enumerate(inpar):
print "01lllllllllllllllllllllllllllllllllllllllllllllllllll"
print i, name
interval[name] = 1.0 / bin_num[name]
bin_num[name] += 1
ntotal *= bin_num[name]
for i in range(n_params): cube.append(0)
sf.Info('Begin grid scan ...')
Naccept = 0
for Nrun in range(ntotal):
iner = 1
for i,name in enumerate(inpar):
print "01lllllllllllllllllllllllllllllllllllllllllllllllllll"
print i,name
cube[i] = ( int(Nrun/iner) )%bin_num[name] * interval[name]
print "Nrun", Nrun
print "iner", iner
print int(Nrun/iner)
print "bin_num", bin_num[name]
print ( int(Nrun/iner) )%bin_num[name]
print "interval", interval[name]
print ( int(Nrun/iner) )%bin_num[name] * interval[name]
print cube[i]
iner *= bin_num[name]
Prior(cube, n_dims, n_params)
#raw_input()
#continue
loglike = LogLikelihood(cube, n_dims, n_params)
if loglike > sf.log_zero:
Naccept += 1
f_out.write('\t'.join([str(x) for x in cube])+'\t'+str(loglike)+'\n')
f_out.flush()
if (Nrun+1)%n_print == 0:
print '------------ Num: %i ------------'%(Nrun+1)
print 'Input par = '+str(cube[0:n_dims])
print 'Output par = '+str(cube[n_dims:n_params])
print ' loglike = '+str(loglike)
print 'Accepted Num = '+str(Naccept)
print 'Total Num = '+str(Nrun+1)
def readrun(LogLikelihood,Prior,n_dims,n_params,inpar,bin_num,n_print,outputfiles_basename,outputfiles_filename):
#print "readrun() in scanmanner.py 01llllllll"
#print outputfiles_basename,outputfiles_filename
f_out = open(os.path.join(outputfiles_basename,outputfiles_filename),'w')
import manfun as mf
Ploter = mf.plot()
Ploter.setPlotPar(outputfiles_basename)
for i,name in enumerate(inpar):
try:
Ploter._data[name]
except:
sf.ErrorStop('Input parameter "%s" could not found in ScanInf.txt.'%name)
for i,name in enumerate(inpar):
ntotal = len(Ploter._data[name])
break
cube = []
for i in range(n_params): cube.append(0)
sf.Info('Begin read scan ...')
Naccept = 0
for Nrun in range(ntotal):
iner = Nrun
for i,name in enumerate(inpar):
cube[i] = Ploter._data[name][iner]
loglike = LogLikelihood(cube, n_dims, n_params)
#if loglike > sf.log_zero:
if True:
Naccept += 1
f_out.write('\t'.join([str(x) for x in cube])+'\t'+str(loglike)+'\n')
f_out.flush()
if (Nrun+1)%n_print == 0:
print '------------ Num: %i ------------'%(Nrun+1)
print 'Input par = '+str(cube[0:n_dims])
print 'Output par = '+str(cube[n_dims:n_params])
print ' loglike = '+str(loglike)
print 'Accepted Num = '+str(Naccept)
print 'Total Num = '+str(Nrun+1)
def ReadIn(Configfile, ES, Programs, CS, Ploter):
cf = ConfigParser.ConfigParser()
cf.read(Configfile)
## Read the basic scan parameters
try:
ES.setScanMethod(cf.get('scan', 'Scan method'))
except ConfigParser.NoOptionError:
sf.WarningWait(
'Can not find "Scan method" in the input configure file, it will take the default value, "Random".'
)
try:
if ES.getScanMethod() == 'PolyChord'.upper(
): # yuanfang modified for parallel polychord
# from random import random
ES.setFileName(cf.get('scan', 'Result file name'))
else:
ES.setFileName(cf.get('scan', 'Result file name'))
except ConfigParser.NoOptionError:
sf.ErrorStop(
'Please provide "Result file name" in the input configure file.')
## If the scan method is 'plot', go directly to the 'plot' section
## Read the plot information
plot_items = cf.options("plot")
if 'histogram' in plot_items:
Ploter.setHistogram(cf.get('plot', 'Histogram'))
if 'scatter' in plot_items:
Ploter.setScatter(cf.get('plot', 'Scatter'))
if 'color' in plot_items:
Ploter.setColor(cf.get('plot', 'Color'))
if 'contour' in plot_items:
Ploter.setContour(cf.get('plot', 'Contour'))
if ES.getScanMethod() == 'PLOT': return float('nan')
## Back to Read the basic scan parameters
try:
ES.setPointNum(cf.getint('scan', 'Points number'))
except ConfigParser.NoOptionError:
sf.WarningWait(
'Can not find "Points number" in the input configure file, it will take the default value, 100.'
)
except ValueError:
sf.ErrorStop(
'The "Points number" in the input configure file must be an integer.'
)
try:
ES.setRandomSeed(cf.getint('scan', 'Random seed'))
except ConfigParser.NoOptionError:
sf.WarningWait(
'Can not find "Random seed" in the input configure file, it will take current system time as ramdom seed.'
)
except ValueError:
sf.ErrorStop(
'The "Random seed" in the input configure file must be an integer.'
)
try:
ES.setPrintNum(cf.getint('scan', 'Interval of print'))
except ConfigParser.NoOptionError:
sf.WarningNoWait(
'Can not find "Interval of print" in the input configure file, it will take the default value, 1.'
)
except ValueError:
sf.WarningNoWait(
'The "Interval of print" in the input configure file must be an integer, it will take the default value, 1.'
)
try:
ES.setInputPar(cf.get('scan', 'Input parametes'))
except ConfigParser.NoOptionError:
sf.ErrorStop(
'Can not find "Input parametes" in the input configure file.')
try:
ES.setAccepRate(cf.get('scan', 'Acceptance rate'))
except ConfigParser.NoOptionError:
pass
## Read the program(s) setting
ProgID = filter(lambda x: x.startswith('program'), cf.sections())
ProgID.sort(key=lambda x: int(filter(str.isdigit, x)))
for ii in ProgID:
items = cf.options(ii)
fullitems = [
'program name', 'execute command', 'command path', 'input file',
'input variable', 'output file', 'output variable'
]
for jj in fullitems:
if not jj in items:
sf.ErrorStop('For "%s", item "%s" missed.' % (ii, jj))
Programs[ii] = mf.program()
Programs[ii].setProgName(cf.get(ii, 'Program name'))
Programs[ii].setCommand(cf.get(ii, 'Execute command'))
Programs[ii].setComPath(cf.get(ii, 'Command path'))
Programs[ii].setInputFile(cf.get(ii, 'Input file'))
Programs[ii].setInputVar(cf.get(ii, 'Input variable'))
Programs[ii].setOutputFile(cf.get(ii, 'Output file'))
Programs[ii].setOutputVar(cf.get(ii, 'Output variable'))
try:
Programs[ii].setRunFlag(cf.get(ii, 'Run flag'))
except:
sf.Info('No Run flag.')
## manage the vars
# ES.setProgID(ProgID)
ES.setProgram(Programs)
## Read the constraints
constraint_items = cf.options("constraint")
sf.Info('...............................................')
sf.Info('...............................................')
sf.Debug('constraint_items', constraint_items)
if 'gaussian' in constraint_items:
CS.setGaussian(cf.get('constraint', 'Gaussian'))
if 'limit' in constraint_items:
CS.setLimit(cf.get('constraint', 'Limit'))
if 'chi^2' in constraint_items:
CS.setLoglike(cf.get('constraint', 'chi^2'))
return ProgID