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fit6.py
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fit6.py
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# PURPOSE: fit inner and outer regions of a cluster
# v3 for entropy/mfe_*
# modification: no more the '_v2' at the end of file names.
# v3sherpa42: modified save_data --> save_table, because in
# sherpa 4.2, save_data produced fits files instead
# of text files
# v5: * based on v3sherpa42
# * changed the guess statement (suspected to have error) to a manual
# way to estimate normalization, taken from ktofr8.py
# * make sure when you call out0 that it's defined. in clusters where
# there is no out region defined, the variable out0 is never
# assigned.
# * fit3_*.ps --> fit5_*.ps
# v6: * same method for both ACIS-S and ACIS-I. for easiness, used same code
# from fit5.py, keeping only the ACIS-S part, and adding the new chip#
# "i" to 5,6,7
# * include spectrum if WARF(ob,ccd,reg) file exists (as opposed to checking
# existence of RMF file)
# OUTPUT: LOCCLU/bestfitnh.txt
# OUTPUT: cluname_TZ.txt and TZ.txt (results appended to file)
# OUTPUT: cluname_normTZ.txt (results appended to file)
# OUTPUT: chi0TZ.txt (results appended to file)
# OUTPUT: errTZ.txt (results appended to file)
# OUTPUT: LOCCLU/spec/srcin.txt and LOCCLU/spec/srcout.txt and LOCCLU/spec/srctot.txt
import glob
import os
import commands
import sherpa
from sherpa.astro.ui import *
from pychips.all import *
def clufit(clu, z, nh) :
locclu = 'mfe_' + clu
emin=0.3
clean()
in2soft = glob.glob(locclu+'/spec/sp*_in2_ccd[i567]_grp.pi')
out2soft = glob.glob(locclu+'/spec/sp*_out2_ccd[i567]_grp.pi')
################################################################################################################
# SOFT CHIPS
################################################################################################################
# Analysis for observations on CCD's 5, 6 and 7 -- region=in
softinobs = []
nobs=1
for i in range(len(in2soft)) :
obs = in2soft[i].rpartition('/')[2].partition('_')[0][2:]
ccds= in2soft[i].rpartition('/')[2].partition('_ccd')[2][0]
scnt=commands.getoutput('dmlist "'+in2soft[i]+'[cols counts]" data,clean')
cntv=scnt.split('\n')
cntv.remove(cntv[0])
for ii in range(len(cntv)) :
cntv[ii]=float(cntv[ii])
if sum(cntv) > 100 and os.path.exists(locclu+'/spec/sp'+obs+'_in2_ccd'+ccds+'.warf'):
softinobs.append(nobs)
print 'LOADING .... '+in2soft[i]+' ------------'
load_pha(nobs, in2soft[i] )
load_rmf(nobs, locclu+'/spec/sp'+obs+'_ccd'+ccds+'_center.wrmf')
load_arf(nobs, locclu+'/spec/sp'+obs+'_in2_ccd'+ccds+'.warf')
load_bkg(nobs, locclu+'/spec/sp'+obs+'_in2_ccd'+ccds+'_bgbg2.pi')
if len(softinobs) == 1 :
in0 = nobs
exec('set_source(nobs, xsphabs.abs1 * xsapec.in' +str(nobs)+')')
exec('in'+str(nobs)+'.kt = 5')
exec('in'+str(nobs)+'.abundanc = .3')
exec('thaw(in'+str(nobs)+'.abundanc)')
exec('in'+str(nobs)+'.redshift = '+str(z) )
else :
exec('set_source(nobs, abs1 * xsapec.in' +str(nobs)+')')
exec('in'+str(nobs)+'.kt = '+'in'+str(in0)+'.kt')
exec('in'+str(nobs)+'.abundanc = '+'in'+str(in0)+'.abundanc')
exec('in'+str(nobs)+'.redshift = '+'in'+str(in0)+'.redshift')
exec 'emnorm0=abs(float(in'+str(nobs)+'.norm.val)*calc_data_sum(id=nobs,lo=0.3,hi=0.7)/calc_model_sum(id=nobs,lo=0.3,hi=0.7))'
exec 'set_par(in'+str(nobs)+'.norm, val=float(emnorm0), min=float(emnorm0/1e3), max=float(emnorm0*1e3) )'
subtract(nobs)
nobs=nobs+1
# Analysis for observations on CCD's 5, 6 and 7 -- region=out
softoutobs = []
for i in range(len(out2soft)) :
obs = out2soft[i].rpartition('/')[2].partition('_')[0][2:]
ccds= out2soft[i].rpartition('/')[2].partition('_ccd')[2][0]
scnt=commands.getoutput('dmlist "'+out2soft[i]+'[cols counts]" data,clean')
cntv=scnt.split('\n')
cntv.remove(cntv[0])
for ii in range(len(cntv)) :
cntv[ii]=float(cntv[ii])
if sum(cntv) > 100 and os.path.exists(locclu+'/spec/sp'+obs+'_out2_ccd'+ccds+'.warf'):
softoutobs.append(nobs)
print 'LOADING .... '+out2soft[i]+' ------------'
load_pha(nobs, out2soft[i] )
load_rmf(nobs, locclu+'/spec/sp'+obs+'_ccd'+ccds+'_center.wrmf')
load_arf(nobs, locclu+'/spec/sp'+obs+'_out2_ccd'+ccds+'.warf')
load_bkg(nobs, locclu+'/spec/sp'+obs+'_out2_ccd'+ccds+'_bgbg2.pi')
if len(softoutobs) == 1 :
out0 = nobs
exec('set_source(nobs, xsphabs.abs1 * xsapec.out' +str(nobs)+')')
exec('out'+str(nobs)+'.kt = 5')
exec('out'+str(nobs)+'.abundanc = .3')
exec('thaw(out'+str(nobs)+'.abundanc)')
exec('out'+str(nobs)+'.redshift = '+str(z) )
else :
exec('set_source(nobs, abs1 * xsapec.out' +str(nobs)+')')
exec('out'+str(nobs)+'.kt = '+'out'+str(out0)+'.kt')
exec('out'+str(nobs)+'.abundanc = '+'out'+str(out0)+'.abundanc')
exec('out'+str(nobs)+'.redshift = '+'out'+str(out0)+'.redshift')
exec 'emnorm0=abs(float(out'+str(nobs)+'.norm.val)*calc_data_sum(id=nobs,lo=0.3,hi=0.7)/calc_model_sum(id=nobs,lo=0.3,hi=0.7))'
exec 'set_par(out'+str(nobs)+'.norm, val=float(emnorm0), min=float(emnorm0/1e3), max=float(emnorm0*1e3) )'
subtract(nobs)
nobs=nobs+1
################################################################################################################
if nobs > 1 :
abs1.nh = nh
abs1.nh.min= nh/5.
abs1.nh.max= nh*5.
# freeze(abs1.nh)
ignore('0:'+str(emin)+', 7:')
fit()
absfile = open(locclu+'/bestfitnh.txt', 'w')
absfile.write(str(abs1.nh.val)+'\n')
absfile.close()
if get_fit_results().rstat > 3 :
print ' ------------------ BAD FIT.. TRY MANUAL FIT --------------------'
cont=''
while cont != 'xxx' :
cont = raw_input ('Enter command>> ')
if cont =='xxx' : break
else :
try : exec cont
except : pass
inobs = softinobs
outobs = softoutobs
# Write the best fit Tin, Zin, Tout Zout and spectrum normalization
print
print 'Writing results to file.. '
print
nresfile = open('cluname_TZ.txt', 'a')
resfile = open('TZ.txt', 'a')
normfile = open('cluname_normTZ.txt', 'a')
if 'out0' in locals() :
exec 'nresfile.write ( clu + " " + str(in'+str(in0)+'.kt.val) + " " + str(in'+str(in0)+'.abundanc.val) + " " + str(out'+str(out0)+'.kt.val) + " " + str(out'+str(out0)+'.abundanc.val) + "\\n" )'
exec 'resfile.write ( str(in'+str(in0)+'.kt.val) + " " + str(in'+str(in0)+'.abundanc.val) + " " + str(out'+str(out0)+'.kt.val) + " " + str(out'+str(out0)+'.abundanc.val) + "\\n" )'
exec 'normfile.write ( clu + " " + str(in'+str(in0)+'.norm.val) + " " + str(out'+str(out0)+'.norm.val) + "\\n" )'
else :
exec 'nresfile.write ( clu + " " + str(in'+str(in0)+'.kt.val) + " " + str(in'+str(in0)+'.abundanc.val) + " -1 -1\\n" )'
exec 'resfile.write ( str(in'+str(in0)+'.kt.val) + " " + str(in'+str(in0)+'.abundanc.val) + " -1 -1\\n" )'
exec 'normfile.write ( clu + " " + str(in'+str(in0)+'.norm.val) + " -1\\n" )'
nresfile.close()
resfile.close()
normfile.close()
# Write the reduced chi squared:
chifile = open('chi0TZ.txt', 'a')
chifile.write(str(get_fit_results().rstat)+'\n')
chifile.close()
# Uncertainties in the parameters
print 'Calculating uncertainties ...'
print
instr=''
for i in range(len(inobs)) : instr = instr + str(inobs[i]) + ','
outstr=''
for i in range(len(outobs)) : outstr = outstr + str(outobs[i]) + ','
class backupproj(object) :
parmins=['NaN','NaN']
parmaxes=['NaN','NaN']
try :
exec 'proj('+instr+' in'+str(in0)+'.kt, in'+str(in0)+'.abundanc)'
resin2 = get_proj_results()
except :
resin2=backupproj()
try :
exec 'proj('+outstr+' out'+str(out0)+'.kt, out'+str(out0)+'.abundanc)'
resout2 = get_proj_results()
except :
resout2=backupproj()
uncfile = open('errTZ.txt', 'a')
# T_in_min T_in_max Z_in_min Z_in_max T_out_min T_out_max Z_out_min Z_out_max
uncfile.write( str(resin2.parmins[0]) + ' ' + str(resin2.parmaxes[0]) + ' ' + str(resin2.parmins[1]) + ' ' + str(resin2.parmaxes[1]) + ' ' + str(resout2.parmins[0]) + ' ' + str(resout2.parmaxes[0]) + ' ' + str(resout2.parmins[1]) + ' ' + str(resout2.parmaxes[1]) + '\n' )
uncfile.close()
# Write the spectra to txt file
print 'Writing source spectrum to file ...'
print
load_arrays('srcin', get_source_plot(in0).xlo, get_source_plot(in0).y )
save_table('srcin', locclu+'/spec/srcin.txt[opt kernel=text/raw]')
if 'out0' in locals() :
load_arrays('srcout', get_source_plot(out0).xlo, get_source_plot(out0).y )
save_table('srcout', locclu+'/spec/srcout.txt[opt kernel=text/raw]')
else : os.system('cp '+locclu+'/spec/srcin.txt '+locclu+'/spec/srcout.txt')
# Save a .PS version of the plots
add_window(11,8.5,'inches')
allobs = inobs + outobs
allobs.sort()
for obs in allobs :
plot_fit_resid(obs)
if os.path.exists('fitplots/fit5_'+clu+'_'+str(obs)+'.ps') : os.remove('fitplots/fit5_'+clu+'_'+str(obs)+'.ps')
print_window ('fitplots/fit5_'+clu+'_'+str(obs), ['format', 'ps', 'orientation', 'landscape'])
# Write the spectrum of entire cluster (in+out regions) to txt file
if 'out0' in locals() :
try : exec 'in'+str(in0)+'.kt = out'+str(out0)+'.kt'
except NameError : pass
try : exec 'in'+str(in0)+'.abundanc = out'+str(out0)+'.abundanc'
except NameError : pass
exec 'fit'+str(tuple(allobs))
load_arrays('srctot', get_source_plot(in0).xlo, get_source_plot(in0).y )
save_table('srctot', locclu+'/spec/srctot.txt[opt kernel=text/raw]')
else : os.system('cp '+locclu+'/spec/srcin.txt '+locclu+'/spec/srctot.txt')
delete_window()