def run(self, evfile, scfile, sra, sdec, rad, bra, bdec, brad, tmin, tmax,
emin, emax, enbin, irfs, cube, outroot, dcostheta, thetamax, binsz,
zmax):
import time
from psfcor import arfcreate
import pyfits
tstart = tmin
tstop = tmax
scf = pyfits.open(scfile)
tstart_sc = float(scf[0].header['TSTART'])
tstop_sc = float(scf[0].header['TSTOP'])
scf.close()
self.putlog(os.environ['PFILES'])
if tstart == "INDEF":
tstart = tstart_sc
else:
try:
tstart = float(tstart)
except:
self.putlog("Warning: Error converting tstart to float.")
self.putlog("Using start time from SC file.")
if tstop == "INDEF":
tstop = tstop_sc
else:
try:
tstop = float(tstop)
except:
self.putlog("Warning: Error converting tstart to float.")
if tstart > tstart_sc: tstart = tstart_sc
if tstop > tstop_sc: tstop = tstop_sc
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(sdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(sdec)+"*#deg)*COS((RA-"+\
str(sra)+")*#deg))/#deg<"+str(rad)+".AND.TIME>"+str(tstart)+".AND.TIME<"+str(tstop)
pid = str(os.getpid())
src_ef = 'ev' + pid + '_src.fits'
bkg_ef = 'ev' + pid + '_bkg.fits'
srcf = outroot + '_src.pha'
bkgf = outroot + '_bkg.pha'
if self.state == "running":
try:
self.putlog(
"***Running FSELECT to produce event file for the source region***"
)
subprocess.call(["fselect", evfile, '!' + src_ef, expr])
except:
self.putlog("Error occured when running FSELECT for src.")
self.stop()
else:
pass
fh = pyfits.open(src_ef, mode='update')
hdu = fh[1].header
hdu['DSVAL2 '] = "CIRCLE(" + str(sra) + "," + str(
sdec) + "," + str(rad) + ")"
fh.close()
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(bdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(bdec)+"*#deg)*COS((RA-"+\
str(bra)+")*#deg))/#deg<"+str(brad)+".AND.TIME>"+str(tstart)+".AND.TIME<"+str(tstop)
if self.state == "running":
try:
self.putlog(
"***Running FSELECT to produce event file for the background region***"
)
subprocess.call(["fselect", evfile, '!' + bkg_ef, expr])
except:
self.putlog("Error occured when running FSELECT for backgrnd.")
self.stop()
if self.state == "running":
self.putlog(
"***Running GTBIN to produce spectrum for the source region***"
)
time.sleep(0.05)
evbin['algorithm'] = 'PHA1'
evbin['ebinalg'] = 'LOG'
evbin['evfile'] = src_ef
evbin['scfile'] = scfile
evbin['outfile'] = srcf
evbin['tstart'] = tstart
evbin['tstop'] = tstop
evbin['emin'] = emin
evbin['emax'] = emax
evbin['enumbins'] = enbin
evbin['chatter'] = '10'
self.putlog(evbin.command())
catchError = "at the top level:"
gterr = False
inf, outf = evbin.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog(
"GTBIN error during source region extraction! Exiting...")
self.state = "stop"
if self.state == "running":
evbin['evfile'] = bkg_ef
evbin['outfile'] = bkgf
self.putlog(
"***Running GTBIN to produce spectrum for the background region***"
)
time.sleep(0.05)
self.putlog(evbin.command())
catchError = "at the top level:"
gterr = False
inf, outf = evbin.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog(
"GTBIN error during background region extraction! Exiting..."
)
self.state = "stop"
# response
fh = pyfits.open(srcf, mode='update')
hdu = fh[1].header
# hdu['DSVAL2 '] = "CIRCLE("+str(sra)+ ","+str(self.analysis.dec)+","+ \
# str(self.analysis.obs_pars["roi"])+")"
if self.state == "running":
self.putlog("***Running gtrspgen (response generator)***")
rspf = outroot + '.rsp'
gtrsp['respalg'] = "PS"
gtrsp['specfile'] = srcf
gtrsp['scfile'] = scfile
gtrsp['thetacut'] = thetamax
gtrsp['outfile'] = rspf
gtrsp['irfs'] = irfs
gtrsp['dcostheta'] = dcostheta
gtrsp['emin'] = 100.0
gtrsp['emax'] = 300000.0
gtrsp['enumbins'] = 100
gtrsp['chatter'] = 0
self.putlog(gtrsp.command())
catchError = "at the top level:"
gterr = False
inf, outf = gtrsp.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
# self.putlog(str(gterr))
inf.close()
outf.close()
if gterr:
self.putlog("GTRSPGEN error! Exiting...")
self.stop()
time.sleep(0.05)
# PSF
if self.state == "running":
self.putlog("***Running gtpsf (PSF generator)***")
psff = outroot + '_psf.fits'
gtpsf['expcube'] = cube
gtpsf['dec'] = sdec
gtpsf['ra'] = sra
gtpsf['outfile'] = psff
gtpsf['irfs'] = irfs
gtpsf['emin'] = 100.0
gtpsf['emax'] = 300000.0
gtpsf['nenergies'] = 101
gtpsf['thetamax'] = thetamax
gtpsf['ntheta'] = int(thetamax / dcostheta)
gtpsf['chatter'] = 0
self.putlog(gtpsf.command())
catchError = "at the top level:"
gterr = False
inf, outf = gtpsf.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog("GTPSF error! Exiting...")
self.stop()
# ARF
if self.state == "running":
arff = outroot + ".arf"
try:
out = arfcreate(arff, rad, rspf, psff)
self.putlog(out)
except:
self.putlog("ARFCREATE error! Exiting...")
self.stop()
hdu['RESPFILE'] = rspf
hdu['BACKFILE'] = bkgf
hdu['ANCRFILE'] = arff
hdu['BACKSCAL'] = 1.0
fh.flush()
fh.close()
fh = pyfits.open(bkgf, mode='update')
hdu = fh[1].header
hdu['BACKSCAL'] = (brad / rad)**2
fh.flush()
fh.close()
# self.logit(out)
# Clean up
try:
os.system('rm -f ' + psff)
os.system('rm -f src' + pid + '*')
os.system('rm -f bkg' + pid + '*')
os.system('rm -f ev' + pid + '*')
os.system('rm -f rsp' + pid + '*')
except:
pass
if self.state == "running": self.state = "done"
if self.state == "stop": self.state = "stopped"
def run(self,evfile,scfile,sra,sdec,rad,bra,bdec,brad,
tmin,tmax,emin,emax,enbin,irfs,cube,outroot,
dcostheta,thetamax,binsz,zmax):
import time
from psfcor import arfcreate
import pyfits
tstart = tmin
tstop = tmax
scf = pyfits.open(scfile)
tstart_sc = float(scf[0].header['TSTART'])
tstop_sc = float(scf[0].header['TSTOP'])
scf.close()
self.putlog(os.environ['PFILES'])
if tstart == "INDEF":
tstart = tstart_sc
else:
try:
tstart = float(tstart)
except:
self.putlog("Warning: Error converting tstart to float.")
self.putlog("Using start time from SC file.")
if tstop == "INDEF":
tstop = tstop_sc
else:
try:
tstop = float(tstop)
except:
self.putlog("Warning: Error converting tstart to float.")
if tstart > tstart_sc: tstart = tstart_sc
if tstop > tstop_sc: tstop = tstop_sc
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(sdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(sdec)+"*#deg)*COS((RA-"+\
str(sra)+")*#deg))/#deg<"+str(rad)+".AND.TIME>"+str(tstart)+".AND.TIME<"+str(tstop)
pid = str(os.getpid())
src_ef = 'ev'+pid+'_src.fits'
bkg_ef = 'ev'+pid+'_bkg.fits'
srcf = outroot+'_src.pha'
bkgf = outroot+'_bkg.pha'
if self.state == "running":
try:
self.putlog("***Running FSELECT to produce event file for the source region***")
subprocess.call(["fselect",evfile,'!'+src_ef,expr])
except:
self.putlog("Error occured when running FSELECT for src.")
self.stop()
else:
pass
fh = pyfits.open(src_ef,mode='update')
hdu = fh[1].header
hdu['DSVAL2 '] = "CIRCLE("+str(sra)+","+str(sdec)+","+str(rad)+")"
fh.close()
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(bdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(bdec)+"*#deg)*COS((RA-"+\
str(bra)+")*#deg))/#deg<"+str(brad)+".AND.TIME>"+str(tstart)+".AND.TIME<"+str(tstop)
if self.state == "running":
try:
self.putlog("***Running FSELECT to produce event file for the background region***")
subprocess.call(["fselect",evfile,'!'+bkg_ef,expr])
except:
self.putlog("Error occured when running FSELECT for backgrnd.")
self.stop()
if self.state == "running":
self.putlog("***Running GTBIN to produce spectrum for the source region***")
time.sleep(0.05)
evbin['algorithm'] = 'PHA1'
evbin['ebinalg'] = 'LOG'
evbin['evfile'] = src_ef
evbin['scfile'] = scfile
evbin['outfile'] = srcf
evbin['tstart'] = tstart
evbin['tstop'] = tstop
evbin['emin'] = emin
evbin['emax'] = emax
evbin['enumbins'] = enbin
evbin['chatter'] = '10'
self.putlog(evbin.command())
catchError = "at the top level:"
gterr = False
inf,outf = evbin.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog("GTBIN error during source region extraction! Exiting...")
self.state = "stop"
if self.state == "running":
evbin['evfile'] = bkg_ef
evbin['outfile'] = bkgf
self.putlog("***Running GTBIN to produce spectrum for the background region***")
time.sleep(0.05)
self.putlog(evbin.command())
catchError = "at the top level:"
gterr = False
inf,outf = evbin.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog("GTBIN error during background region extraction! Exiting...")
self.state = "stop"
# response
fh = pyfits.open(srcf,mode='update')
hdu = fh[1].header
# hdu['DSVAL2 '] = "CIRCLE("+str(sra)+ ","+str(self.analysis.dec)+","+ \
# str(self.analysis.obs_pars["roi"])+")"
if self.state == "running":
self.putlog( "***Running gtrspgen (response generator)***")
rspf = outroot+'.rsp'
gtrsp['respalg'] = "PS"
gtrsp['specfile'] = srcf
gtrsp['scfile'] = scfile
gtrsp['thetacut'] = thetamax
gtrsp['outfile'] = rspf
gtrsp['irfs'] = irfs
gtrsp['dcostheta'] = dcostheta
gtrsp['emin'] = 100.0
gtrsp['emax'] = 300000.0
gtrsp['enumbins'] = 100
gtrsp['chatter'] = 0
self.putlog(gtrsp.command())
catchError = "at the top level:"
gterr = False
inf,outf = gtrsp.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
# self.putlog(str(gterr))
inf.close()
outf.close()
if gterr:
self.putlog("GTRSPGEN error! Exiting...")
self.stop()
time.sleep(0.05)
# PSF
if self.state == "running":
self.putlog("***Running gtpsf (PSF generator)***")
psff = outroot+'_psf.fits'
gtpsf['expcube'] = cube
gtpsf['dec'] = sdec
gtpsf['ra'] = sra
gtpsf['outfile'] = psff
gtpsf['irfs'] = irfs
gtpsf['emin'] = 100.0
gtpsf['emax'] = 300000.0
gtpsf['nenergies'] = 101
gtpsf['thetamax'] = thetamax
gtpsf['ntheta'] = int(thetamax/dcostheta)
gtpsf['chatter'] = 0
self.putlog(gtpsf.command())
catchError = "at the top level:"
gterr = False
inf,outf = gtpsf.runWithOutput(print_command=False)
for line in outf:
self.putlog(line)
if line.find(catchError) != -1:
gterr = True
inf.close()
outf.close()
if gterr:
self.putlog("GTPSF error! Exiting...")
self.stop()
# ARF
if self.state == "running":
arff = outroot+".arf"
try:
out = arfcreate(arff,rad,rspf,psff)
self.putlog(out)
except:
self.putlog("ARFCREATE error! Exiting..." )
self.stop()
hdu['RESPFILE'] = rspf
hdu['BACKFILE'] = bkgf
hdu['ANCRFILE'] = arff
hdu['BACKSCAL'] = 1.0
fh.flush()
fh.close()
fh = pyfits.open(bkgf,mode='update')
hdu = fh[1].header
hdu['BACKSCAL'] = (brad/rad)**2
fh.flush()
fh.close()
# self.logit(out)
# Clean up
try:
os.system('rm -f '+psff)
os.system('rm -f src'+pid+'*')
os.system('rm -f bkg'+pid+'*')
os.system('rm -f ev'+pid+'*')
os.system('rm -f rsp'+pid+'*')
except:
pass
if self.state == "running": self.state = "done"
if self.state == "stop": self.state = "stopped"
def run(self, evfile, scfile, sra, sdec, rad, bra, bdec, brad, cube, tbin,
irfs, tstart, tstop, emin, emax, enbin, outfile, dcostheta,
thetamax, binsz, zmax, pl_index, index_free, logfile):
''' Given the LAT dat event file (evfile), source and background regions,
Generates a full flux curve using xspec fits for every interval.
Parameters:
evfile - observation event file, create with gtmktime
scfile - observation house keeping file
sra - source RA
sdec - source DEC
rad - source RAD (degrees)
bra - background RA
bdec - background DEC
brad - background region radius
outfile [lc.fits] - output lightcurve FITS file
tbin [86400] - final flux curve time binnig (sec).
tstart [INDEF] - start time (MET sec). If INDEF the value is taken from the evfile.
tstop [INDEF] - start time (MET sec). If INDEF the value is taken from the evfile.
emin [100.0] - lower energy limit of the energy interval (MeV).
emin [300000.0] - upper energy of the energy interval (MeV).
enbin [20] - number of the energy bins to use in xspec fits.
cube - the galactic cube file. If not given or does not exist - it will be
calculated (takes a long time!!!).
binsz [1.0], zmax [100.0] - corresponding gtltcube parameters if a cube is to be calculated.
thetamax [60.0],dcostheta [0.05] - corresponding parameters for psf and response calculations.
See gtpsf,gtrspgen help for details.
pl_index [2.5] - starting value for the photon index of the power law fits
to data.
index_free [False] - if False the index is fixed at pl_index value
'''
logf = open(logfile, "w")
res_str = ""
scf = pyfits.open(scfile)
tstart_sc = float(scf[0].header['TSTART'])
tstop_sc = float(scf[0].header['TSTOP'])
if tstart == "INDEF":
tstart = tstart_sc
else:
try:
tstart = float(tstart)
except:
res_str += "Warning: Error converting tstart to float.\n"
res_str += "Using start time from SC file."
self.putlog("Warning: Error converting tstart to float.")
self.putlog("Using start time from SC file.")
if tstop == "INDEF":
tstop = tstop_sc
else:
try:
tstop = float(tstop)
except:
res_str += "Warning: Error converting tstop to float.\n"
res_str += "Using stop time from SC file.\n"
self.putlog("Warning: Error converting tstart to float.")
logf.write("Using stop time from SC file.\n")
try:
tbin = float(tbin)
except:
res_str += "Warning: Error converting tbin to float.\n"
self.putlog("Warning: Error converting tbin to float.")
logf.close()
return -1, res_str
if tbin < 0.0:
res_str += "Negative tbin. Exit!.\n"
logf.write("Negative tbin. Exit!.\n")
logf.close()
self.putlog("Negative tbin. Exit!.")
return -1, res_str
if tstart > tstart_sc: tstart = tstart_sc
if tstop > tstop_sc: tstop = tstop_sc
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(sdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(sdec)+"*#deg)*COS((RA-"+\
str(sra)+")*#deg))/#deg<"+str(rad)
pid = str(os.getpid())
src_ef = 'ev' + pid + '_src.fits'
bkg_ef = 'ev' + pid + '_bkg.fits'
if self.state == "running":
try:
subprocess.call(["fselect", evfile, '!' + src_ef, expr])
except:
res_str += "Error occured when running FSELECT for src.\n"
self.putlog("Error occured when running FSELECT for src.")
else:
res_str += "Src events extraction OK.\n"
# putlog("Src events extraction OK.")
fh = pyfits.open(src_ef, mode='update')
hdu = fh[1].header
hdu['DSVAL2 '] = "CIRCLE(" + str(sra) + "," + str(sdec) + ",25.0)"
fh.close()
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(bdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(bdec)+"*#deg)*COS((RA-"+\
str(bra)+")*#deg))/#deg<"+str(brad)
if self.state == "running":
try:
subprocess.call(["fselect", evfile, '!' + bkg_ef, expr])
except:
res_str += "Error occured when running FSELECT for backgrnd.\n"
self.putlog("Error occured when running FSELECT for backgrnd.")
else:
res_str += "Bkg extraction OK.\n"
# putlog("Bkg extraction OK.")
# ltcube
if self.state == "running":
cubecalc = False
if not os.path.exists(cube): cubecalc = True
if cubecalc:
gtcube['evfile'] = src_ef
gtcube['scfile'] = scfile
gtcube['outfile'] = cube
gtcube['dcostheta'] = dcostheta
gtcube['binsz'] = binsz
gtcube['zmax'] = zmax
res_str += gtcube.command()
out = gtcube.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += out.read()
logf.write(xxx)
t1 = tstart
t2 = t1 + tbin
nsp = 0
# psf
if self.state == "running":
psff = 'psf' + pid + '.fits'
gtpsf['expcube'] = cube
gtpsf['dec'] = sdec
gtpsf['ra'] = sra
gtpsf['outfile'] = psff
gtpsf['irfs'] = irfs
gtpsf['emin'] = 100.0
gtpsf['emax'] = 300000.0
gtpsf['nenergies'] = 101
gtpsf['thetamax'] = thetamax
gtpsf['ntheta'] = int(thetamax / dcostheta)
gtpsf['chatter'] = 0
res_str += gtpsf.command()
out = gtpsf.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += xxx
logf.write(xxx)
# openning xspec session
try:
os.system('rm -f xspec' + pid + '_lc.txt')
os.system('touch xspec' + pid + '_lc.txt')
except:
pass
arff = 'arf' + pid + '.arf'
# response
hdu0 = fh[0].header
cflux = -9.0
# flexp = pyfits.open('gtbin.lc')
# lcdata = flexp[1].data
ind10 = int(0)
ind25 = int(0)
ind50 = int(0)
ind75 = int(0)
# self.putlog('Lightcurve thread: Sarting the main loop')
# Main loop
nbin = (tstop - tstart) / tbin
while t1 < tstop and self.state == "running":
if (t1 - tstart) / tbin > 0.1 * nbin and ind10 == 0:
self.putlog("Progress: 10%")
ind10 = 1
if (t1 - tstart) / tbin > 0.25 * nbin and ind25 == 0:
self.putlog("Progress: 25%")
ind25 = 1
if (t1 - tstart) / tbin > 0.5 * nbin and ind50 == 0:
self.putlog("Progress: 50%")
ind50 = 1
if (t1 - tstart) / tbin > 0.75 * nbin and ind75 == 0:
self.putlog("Progress: 75%")
ind75 = 1
# self.putlog('Sarting loop '+str(nsp))
logf.write("Interval: " + str(nsp) + " Tstart = " + str(t1) +
" Tstop = " + str(t2) + "\n")
expr = "TIME>" + str(t1) + ".AND.TIME<" + str(t2)
sef1 = 'ev' + pid + '_src' + str(nsp) + '_1.fits'
bef1 = 'ev' + pid + '_bkg' + str(nsp) + '_1.fits'
try:
subprocess.call(["fselect", src_ef, '!' + sef1, expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
try:
subprocess.call(["fselect", bkg_ef, '!' + bef1, expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
expr = "START>" + str(t1) + ".AND.STOP<" + str(t2)
sef = 'ev' + pid + '_src' + str(nsp) + '.fits'
bef = 'ev' + pid + '_bkg' + str(nsp) + '.fits'
try:
subprocess.call(["fselect", sef1 + '+2', '!' + sef, expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
try:
subprocess.call(["fselect", bef1 + '+2', '!' + bef, expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
self.putlog("Error occured when running FSELECT for src.")
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
srcf = 'src' + pid + str(nsp) + '.pha'
evbin['algorithm'] = 'PHA1'
evbin['ebinalg'] = 'LOG'
evbin['evfile'] = sef
evbin['scfile'] = scfile
evbin['outfile'] = srcf
evbin['tstart'] = t1
evbin['tstop'] = t2
evbin['emin'] = emin
evbin['emax'] = emax
evbin['enumbins'] = enbin
evbin['chatter'] = '10'
res = evbin.runWithOutput(print_command=False)[1]
xxx = res.read()
res_str += xxx
# logf.write(xxx+"\n")
bkgf = 'bkg' + pid + str(nsp) + '.pha'
evbin['evfile'] = bef
evbin['outfile'] = bkgf
res = evbin.runWithOutput(print_command=False)[1]
xxx = res.read()
res_str += xxx
# logf.write(xxx+"\n")
# response
if 1:
# if nsp == 0:
rspf = 'rsp' + pid + str(nsp) + '.rsp'
gtrsp['respalg'] = "PS"
gtrsp['specfile'] = srcf
gtrsp['scfile'] = scfile
gtrsp['thetacut'] = thetamax
gtrsp['outfile'] = rspf
gtrsp['irfs'] = irfs
gtrsp['dcostheta'] = dcostheta
gtrsp['emin'] = 100.0
gtrsp['emax'] = 300000.0
gtrsp['enumbins'] = 100
gtrsp['chatter'] = 0
xxx = gtrsp.command()
res_str += xxx
# logf.write(xxx+"\n")
out = gtrsp.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += xxx
# logf.write(xxx+"\n")
if nsp == 0:
arfcreate(arff, rad, rspf, psff)
# Write keywords to source spectrum file
sp.call(['fparkey', bkgf, srcf, 'BACKFILE'])
sp.call(['fparkey', rspf, srcf, 'RESPFILE'])
sp.call(['fparkey', arff, srcf, 'ANCRFILE'])
sp.call(['fparkey', '1.0', srcf, 'BACKSCAL'])
sp.call(
['fparkey',
str((self.brad / self.srad)**2), bkgf, 'BACKSCAL'])
time.sleep(0.05)
if not os.path.exists(srcf) or not os.path.exists(bkgf) or \
not os.path.exists(arff) or not os.path.exists(rspf):
self.state = "stop"
self.putlog(
"Lightcurve extractor: something wrong, files are missing. Stoping."
)
if self.state != "running": break
xspecf = open('xspec' + pid + str(nsp) + '.xcm', 'w')
xspecf.write('log xspec' + pid + str(nsp) + '.log\n')
xspecf.write('query yes\n')
xspecf.write('data 1 ' + srcf + ' \n')
xspecf.write('notice 1:' + str(emin * 1000.0) + '-' +
str(emax * 1000.0) + ' \n')
xspecf.write('ignore 1: **-' + str(emin * 1000.0) + ' ' +
str(emax * 1000.0) + '-** \n')
if index_free:
xspecf.write("model cpflux*pow & "+str(emin*1000.0)+" -1 0 0 1e10 1e10 & "+\
str(emax*1000.0)+" -1 0 0 1e16 1e16 & {0} 0.01 & {1} 0.01 & 1.0 -1 & \n".\
format(cflux,pl_index))
else:
xspecf.write("model cpflux*pow & "+str(emin*1000.0)+" -1 0 0 1e10 1e10 & "+\
str(emax*1000.0)+" -1 0 0 1e10 1e10 & {0} 0.01 & {1} -1 & 1.0 -1 & \n".\
format(cflux,pl_index))
xspecf.write('renorm\n')
xspecf.write('fit 500\n')
xspecf.write('tclout param 3\n')
xspecf.write('set cf [lindex $xspec_tclout 0]\n')
xspecf.write('tclout param 4\n')
xspecf.write('set pl [lindex $xspec_tclout 0]\n')
xspecf.write('error max 1000000.0 3\n')
xspecf.write('tclout error 3\n')
xspecf.write('set cferr [lrange $xspec_tclout 0 1]\n')
if index_free:
xspecf.write('error 4\n')
xspecf.write('tclout error 4\n')
xspecf.write('set plerr [lrange $xspec_tclout 0 1]\n')
else:
xspecf.write('set plerr "0.0 0.0"\n')
# xspr.stdin.write('tclout statistic\n')
# xspr.stdin.write('set chi $xspec_tclout\n')
xspecf.write('catch {exec echo ' + str(0.5 * (t1 + t2)) + " " +
str(0.5 *
(t2 - t1)) + ' $cf $cferr $pl $plerr > xspec_lc' +
pid + str(nsp) + '.txt } \n')
xspecf.write('quit\n')
xspecf.write('yes\n')
xspecf.close()
xspr = sp.Popen(['xspec', 'xspec' + pid + str(nsp) + '.xcm'],
stdout=sp.PIPE,
stdin=sp.PIPE,
stderr=sp.STDOUT)
# xspr = sp.call(['xspec','xspec'+str(nsp)+'.xcm'])
out = xspr.communicate()
os.system('cat xspec_lc' + pid + str(nsp) + '.txt >> xspec' + pid +
'_lc.txt')
nsp += 1
t1 += tbin
t2 = min(tstop, t1 + tbin)
# End of the main loop
# fh.close()
if self.state == "running":
flis = open('cols.lis', 'w')
flis.write('TIME E\n')
flis.write('TIMEDEL E\n')
flis.write('FLUX E\n')
flis.write('LOGFMIN E\n')
flis.write('LOGFMAX E\n')
flis.write('INDEX E\n')
flis.write('INDMIN E\n')
flis.write('INDMAX E\n')
flis.close()
fhead = open('head.lis', 'w')
fhead.write(
'TELESCOP GLAST / name of telescope generating data\n')
fhead.write('INSTRUME LAT / name of instrument generating data\n')
fhead.write('CREATOR LATSPEC / Software creating file\n')
fhead.write('EMIN ' + str(emin) + ' / Lower energy limit, Mev\n')
fhead.write('EMAX ' + str(emax) + ' / Upper energy limit, Mev\n')
fhead.close()
sp.call(["rm", '-f', 'lc1.fits', 'lc2.fits'])
pr1 = sp.Popen([
"fcreate", 'cols.lis', 'xspec' + pid + '_lc.txt',
'lc' + pid + '1.fits', "headfile=head.lis"
])
pr1.wait()
# time.sleep(0.01)
# pr2.wait()
# time.sleep(0.01)
pr3 = sp.Popen([
"fcalc", 'lc' + pid + '1.fits', 'lc' + pid + '2.fits', 'ERROR',
'0.5*(LOGFMAX-LOGFMIN)'
])
# out = pr3.communicate()
pr3.wait()
os.system('rm -f ' + outfile)
pr2 = sp.Popen([
"fcalc", 'lc' + pid + '2.fits', outfile, 'INDEXERR',
'0.5*(INDMAX-INDMIN)'
])
pr2.wait()
# Clean up
sp.call(["rm", '-f', 'lc' + pid + '1.fits', 'lc' + pid + '2.fits'])
os.system('rm -f ' + arff)
os.system('rm -f ' + psff)
os.system('rm -f src' + pid + '*')
os.system('rm -f bkg' + pid + '*')
os.system('rm -f ev' + pid + '*')
os.system('rm -f xspec_lc' + pid + '*')
os.system('rm -f xspec' + pid + '*')
os.system('rm -f rsp' + pid + '*')
# os.system('rm -f lc1.fits')
# os.system('rm -f lc2.fits')
logf.close()
if self.state == "running": self.state = "done"
if self.state == "stop": self.state = "stopped"
def run(self,evfile,scfile,sra,sdec,rad,bra,bdec,brad,
cube,tbin,irfs,tstart,tstop,emin,
emax,enbin,outfile,
dcostheta,thetamax,binsz,zmax,
pl_index,index_free,logfile):
''' Given the LAT dat event file (evfile), source and background regions,
Generates a full flux curve using xspec fits for every interval.
Parameters:
evfile - observation event file, create with gtmktime
scfile - observation house keeping file
sra - source RA
sdec - source DEC
rad - source RAD (degrees)
bra - background RA
bdec - background DEC
brad - background region radius
outfile [lc.fits] - output lightcurve FITS file
tbin [86400] - final flux curve time binnig (sec).
tstart [INDEF] - start time (MET sec). If INDEF the value is taken from the evfile.
tstop [INDEF] - start time (MET sec). If INDEF the value is taken from the evfile.
emin [100.0] - lower energy limit of the energy interval (MeV).
emin [300000.0] - upper energy of the energy interval (MeV).
enbin [20] - number of the energy bins to use in xspec fits.
cube - the galactic cube file. If not given or does not exist - it will be
calculated (takes a long time!!!).
binsz [1.0], zmax [100.0] - corresponding gtltcube parameters if a cube is to be calculated.
thetamax [60.0],dcostheta [0.05] - corresponding parameters for psf and response calculations.
See gtpsf,gtrspgen help for details.
pl_index [2.5] - starting value for the photon index of the power law fits
to data.
index_free [False] - if False the index is fixed at pl_index value
'''
logf = open(logfile,"w")
res_str = ""
scf = pyfits.open(scfile)
tstart_sc = float(scf[0].header['TSTART'])
tstop_sc = float(scf[0].header['TSTOP'])
if tstart == "INDEF":
tstart = tstart_sc
else:
try:
tstart = float(tstart)
except:
res_str += "Warning: Error converting tstart to float.\n"
res_str += "Using start time from SC file."
self.putlog("Warning: Error converting tstart to float.")
self.putlog("Using start time from SC file.")
if tstop == "INDEF":
tstop = tstop_sc
else:
try:
tstop = float(tstop)
except:
res_str += "Warning: Error converting tstop to float.\n"
res_str += "Using stop time from SC file.\n"
self.putlog("Warning: Error converting tstart to float.")
logf.write("Using stop time from SC file.\n")
try:
tbin = float(tbin)
except:
res_str += "Warning: Error converting tbin to float.\n"
self.putlog("Warning: Error converting tbin to float.")
logf.close()
return -1,res_str
if tbin < 0.0:
res_str += "Negative tbin. Exit!.\n"
logf.write("Negative tbin. Exit!.\n")
logf.close()
self.putlog("Negative tbin. Exit!.")
return -1,res_str
if tstart > tstart_sc: tstart = tstart_sc
if tstop > tstop_sc: tstop = tstop_sc
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(sdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(sdec)+"*#deg)*COS((RA-"+\
str(sra)+")*#deg))/#deg<"+str(rad)
pid = str(os.getpid())
src_ef = 'ev'+pid+'_src.fits'
bkg_ef = 'ev'+pid+'_bkg.fits'
if self.state == "running":
try:
subprocess.call(["fselect",evfile,'!'+src_ef,expr])
except:
res_str += "Error occured when running FSELECT for src.\n"
self.putlog("Error occured when running FSELECT for src.")
else:
res_str += "Src events extraction OK.\n"
# putlog("Src events extraction OK.")
fh = pyfits.open(src_ef,mode='update')
hdu = fh[1].header
hdu['DSVAL2 '] = "CIRCLE("+str(sra)+","+str(sdec)+",25.0)"
fh.close()
expr = "ARCCOS(SIN(DEC*#deg)*SIN("+str(bdec)+\
"*#deg)+COS(DEC*#deg)*COS("+str(bdec)+"*#deg)*COS((RA-"+\
str(bra)+")*#deg))/#deg<"+str(brad)
if self.state == "running":
try:
subprocess.call(["fselect",evfile,'!'+bkg_ef,expr])
except:
res_str += "Error occured when running FSELECT for backgrnd.\n"
self.putlog("Error occured when running FSELECT for backgrnd.")
else:
res_str += "Bkg extraction OK.\n"
# putlog("Bkg extraction OK.")
# ltcube
if self.state == "running":
cubecalc = False
if not os.path.exists(cube): cubecalc = True
if cubecalc:
gtcube['evfile'] = src_ef
gtcube['scfile'] = scfile
gtcube['outfile'] = cube
gtcube['dcostheta'] = dcostheta
gtcube['binsz'] = binsz
gtcube['zmax'] = zmax
res_str += gtcube.command()
out = gtcube.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += out.read()
logf.write(xxx)
t1 = tstart
t2 = t1+tbin
nsp = 0
# psf
if self.state == "running":
psff = 'psf'+pid+'.fits'
gtpsf['expcube'] = cube
gtpsf['dec'] = sdec
gtpsf['ra'] = sra
gtpsf['outfile'] = psff
gtpsf['irfs'] = irfs
gtpsf['emin'] = 100.0
gtpsf['emax'] = 300000.0
gtpsf['nenergies'] = 101
gtpsf['thetamax'] = thetamax
gtpsf['ntheta'] = int(thetamax/dcostheta)
gtpsf['chatter'] = 0
res_str += gtpsf.command()
out = gtpsf.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += xxx
logf.write(xxx)
# openning xspec session
try:
os.system('rm -f xspec'+pid+'_lc.txt')
os.system('touch xspec'+pid+'_lc.txt')
except:
pass
arff = 'arf'+pid+'.arf'
# response
hdu0 = fh[0].header
cflux = -9.0
# flexp = pyfits.open('gtbin.lc')
# lcdata = flexp[1].data
ind10 = int(0)
ind25 = int(0)
ind50 = int(0)
ind75 = int(0)
# self.putlog('Lightcurve thread: Sarting the main loop')
# Main loop
nbin = (tstop - tstart)/tbin
while t1<tstop and self.state == "running":
if (t1 - tstart)/tbin > 0.1*nbin and ind10 == 0:
self.putlog("Progress: 10%")
ind10 = 1
if (t1 - tstart)/tbin > 0.25*nbin and ind25 == 0:
self.putlog("Progress: 25%")
ind25 = 1
if (t1 - tstart)/tbin > 0.5*nbin and ind50 == 0:
self.putlog("Progress: 50%")
ind50 = 1
if (t1 - tstart)/tbin > 0.75*nbin and ind75 == 0:
self.putlog("Progress: 75%")
ind75 = 1
# self.putlog('Sarting loop '+str(nsp))
logf.write("Interval: "+str(nsp)+" Tstart = "+str(t1)+" Tstop = "+str(t2)+"\n")
expr = "TIME>"+str(t1)+".AND.TIME<"+str(t2)
sef1 = 'ev'+pid+'_src'+str(nsp)+'_1.fits'
bef1 = 'ev'+pid+'_bkg'+str(nsp)+'_1.fits'
try:
subprocess.call(["fselect",src_ef,'!'+sef1,expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
try:
subprocess.call(["fselect",bkg_ef,'!'+bef1,expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
expr = "START>"+str(t1)+".AND.STOP<"+str(t2)
sef = 'ev'+pid+'_src'+str(nsp)+'.fits'
bef = 'ev'+pid+'_bkg'+str(nsp)+'.fits'
try:
subprocess.call(["fselect",sef1+'+2','!'+sef,expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
try:
subprocess.call(["fselect",bef1+'+2','!'+bef,expr])
except:
xxx = "Error occured when running FSELECT for src.\n"
self.putlog("Error occured when running FSELECT for src.")
res_str += xxx
# logf.write(xxx)
else:
xxx = "Src events extraction OK.\n"
res_str += xxx
# logf.write(xxx)
srcf = 'src'+pid+str(nsp)+'.pha'
evbin['algorithm'] = 'PHA1'
evbin['ebinalg'] = 'LOG'
evbin['evfile'] = sef
evbin['scfile'] = scfile
evbin['outfile'] = srcf
evbin['tstart'] = t1
evbin['tstop'] = t2
evbin['emin'] = emin
evbin['emax'] = emax
evbin['enumbins'] = enbin
evbin['chatter'] = '10'
res = evbin.runWithOutput(print_command=False)[1]
xxx = res.read()
res_str += xxx
# logf.write(xxx+"\n")
bkgf = 'bkg'+pid+str(nsp)+'.pha'
evbin['evfile'] = bef
evbin['outfile'] = bkgf
res = evbin.runWithOutput(print_command=False)[1]
xxx = res.read()
res_str += xxx
# logf.write(xxx+"\n")
# response
if 1:
# if nsp == 0:
rspf = 'rsp'+pid+str(nsp)+'.rsp'
gtrsp['respalg'] = "PS"
gtrsp['specfile'] = srcf
gtrsp['scfile'] = scfile
gtrsp['thetacut'] = thetamax
gtrsp['outfile'] = rspf
gtrsp['irfs'] = irfs
gtrsp['dcostheta'] = dcostheta
gtrsp['emin'] = 100.0
gtrsp['emax'] = 300000.0
gtrsp['enumbins'] = 100
gtrsp['chatter'] = 0
xxx = gtrsp.command()
res_str += xxx
# logf.write(xxx+"\n")
out = gtrsp.runWithOutput(print_command=False)[1]
xxx = out.read()
res_str += xxx
# logf.write(xxx+"\n")
if nsp == 0:
arfcreate(arff,rad,rspf,psff)
# Write keywords to source spectrum file
sp.call(['fparkey',bkgf,srcf,'BACKFILE'])
sp.call(['fparkey',rspf,srcf,'RESPFILE'])
sp.call(['fparkey',arff,srcf,'ANCRFILE'])
sp.call(['fparkey','1.0',srcf,'BACKSCAL'])
sp.call(['fparkey',str((self.brad/self.srad)**2),bkgf,'BACKSCAL'])
time.sleep(0.05)
if not os.path.exists(srcf) or not os.path.exists(bkgf) or \
not os.path.exists(arff) or not os.path.exists(rspf):
self.state = "stop"
self.putlog("Lightcurve extractor: something wrong, files are missing. Stoping.")
if self.state != "running": break
xspecf = open('xspec'+pid+str(nsp)+'.xcm','w')
xspecf.write('log xspec'+pid+str(nsp)+'.log\n')
xspecf.write('query yes\n')
xspecf.write('data 1 '+srcf+' \n')
xspecf.write('notice 1:'+str(emin*1000.0)+'-'+str(emax*1000.0)+' \n')
xspecf.write('ignore 1: **-'+str(emin*1000.0)+' '+str(emax*1000.0)+'-** \n')
if index_free:
xspecf.write("model cpflux*pow & "+str(emin*1000.0)+" -1 0 0 1e10 1e10 & "+\
str(emax*1000.0)+" -1 0 0 1e16 1e16 & {0} 0.01 & {1} 0.01 & 1.0 -1 & \n".\
format(cflux,pl_index))
else:
xspecf.write("model cpflux*pow & "+str(emin*1000.0)+" -1 0 0 1e10 1e10 & "+\
str(emax*1000.0)+" -1 0 0 1e10 1e10 & {0} 0.01 & {1} -1 & 1.0 -1 & \n".\
format(cflux,pl_index))
xspecf.write('renorm\n')
xspecf.write('fit 500\n')
xspecf.write('tclout param 3\n')
xspecf.write('set cf [lindex $xspec_tclout 0]\n')
xspecf.write('tclout param 4\n')
xspecf.write('set pl [lindex $xspec_tclout 0]\n')
xspecf.write('error max 1000000.0 3\n')
xspecf.write('tclout error 3\n')
xspecf.write('set cferr [lrange $xspec_tclout 0 1]\n')
if index_free:
xspecf.write('error 4\n')
xspecf.write('tclout error 4\n')
xspecf.write('set plerr [lrange $xspec_tclout 0 1]\n')
else:
xspecf.write('set plerr "0.0 0.0"\n')
# xspr.stdin.write('tclout statistic\n')
# xspr.stdin.write('set chi $xspec_tclout\n')
xspecf.write('catch {exec echo '+str(0.5*(t1+t2))+" "+str(0.5*(t2-t1))+' $cf $cferr $pl $plerr > xspec_lc'+pid+str(nsp)+'.txt } \n')
xspecf.write('quit\n')
xspecf.write('yes\n')
xspecf.close()
xspr = sp.Popen(['xspec','xspec'+pid+str(nsp)+'.xcm'],stdout=sp.PIPE,stdin=sp.PIPE,stderr=sp.STDOUT)
# xspr = sp.call(['xspec','xspec'+str(nsp)+'.xcm'])
out = xspr.communicate()
os.system('cat xspec_lc'+pid+str(nsp)+'.txt >> xspec'+pid+'_lc.txt')
nsp += 1
t1 += tbin
t2 = min(tstop,t1+tbin)
# End of the main loop
# fh.close()
if self.state == "running":
flis = open('cols.lis','w')
flis.write('TIME E\n')
flis.write('TIMEDEL E\n')
flis.write('FLUX E\n')
flis.write('LOGFMIN E\n')
flis.write('LOGFMAX E\n')
flis.write('INDEX E\n')
flis.write('INDMIN E\n')
flis.write('INDMAX E\n')
flis.close()
fhead = open('head.lis','w')
fhead.write('TELESCOP GLAST / name of telescope generating data\n')
fhead.write('INSTRUME LAT / name of instrument generating data\n')
fhead.write('CREATOR LATSPEC / Software creating file\n')
fhead.write('EMIN '+str(emin)+' / Lower energy limit, Mev\n')
fhead.write('EMAX '+str(emax)+' / Upper energy limit, Mev\n')
fhead.close()
sp.call(["rm",'-f','lc1.fits','lc2.fits'])
pr1 = sp.Popen(["fcreate",'cols.lis','xspec'+pid+'_lc.txt','lc'+pid+'1.fits',"headfile=head.lis"])
pr1.wait()
# time.sleep(0.01)
# pr2.wait()
# time.sleep(0.01)
pr3 = sp.Popen(["fcalc",'lc'+pid+'1.fits','lc'+pid+'2.fits','ERROR','0.5*(LOGFMAX-LOGFMIN)'])
# out = pr3.communicate()
pr3.wait()
os.system('rm -f '+outfile)
pr2 = sp.Popen(["fcalc",'lc'+pid+'2.fits',outfile,'INDEXERR','0.5*(INDMAX-INDMIN)'])
pr2.wait()
# Clean up
sp.call(["rm",'-f','lc'+pid+'1.fits','lc'+pid+'2.fits'])
os.system('rm -f '+arff)
os.system('rm -f '+psff)
os.system('rm -f src'+pid+'*')
os.system('rm -f bkg'+pid+'*')
os.system('rm -f ev'+pid+'*')
os.system('rm -f xspec_lc'+pid+'*')
os.system('rm -f xspec'+pid+'*')
os.system('rm -f rsp'+pid+'*')
# os.system('rm -f lc1.fits')
# os.system('rm -f lc2.fits')
logf.close()
if self.state == "running": self.state = "done"
if self.state == "stop": self.state = "stopped"
