def do_fitprof(datafile):
"""Run IRAF fitprof routine to measure line centers and widths.
For each line specified in the module header generate the necessary inputs
to fitprof and execture the routine. The fitting regions are also
specified in the module header.
Parameters
----------
datafile : str
Name of a multispec fits file to pass as input to fitprof. Must have a WCS solution in the header.
Returns
-------
None
Nothing is returned. Instead, IRAF writes the results to a file.
"""
for l, cl, r in zip(llist,centlist,rlist):
with open('{}.lines'.format(l),'w') as f:
print l
for c in cl:
f.write('{} INDEF g\n'.format(c))
iraf.fitprofs(datafile,
region=r,
positio='{}.lines'.format(l),
logfile='{}.fitp'.format(l))
return
def do_fitprof(datafile, pointing):
"""Run IRAF fitprof routine to measure line centers and widths.
For each line specified in the module header generate the necessary inputs
to fitprof and execture the routine. The fitting regions are also
specified in the module header.
Parameters
----------
datafile : str
Name of a multispec fits file to pass as input to fitprof. Must have a WCS solution in the header.
Returns
-------
None
Nothing is returned. Instead, IRAF writes the results to a file.
"""
dirn = os.path.dirname(datafile)
if len(dirn) > 0:
dirn += '/'
for l, cl, r in zip(llist, centlist, rlist):
with open('{}P{}_{}.lines'.format(dirn,pointing,l),'w') as f:
for c in cl:
f.write('{:4.2f} INDEF g 15\n'.format(c))
proffile = '{}P{}_{}.fitp'.format(dirn,pointing,l)
if os.path.exists(proffile):
print 'Removing ' + proffile
os.system('rm '+proffile)
os.system('rm {}P{}_{}_fits.fits'.format(dirn,pointing,l))
os.system('rm {}P{}_{}_fits.pt'.format(dirn,pointing,l))
try:
iraf.fitprofs(datafile,
region='{:4.0f} {:4.0f}'.format(*r),
positio='{}P{}_{}.lines'.format(dirn,pointing,l),
logfile='{}P{}_{}.fitp'.format(dirn,pointing,l),
fitpositions='single',
fitgfwhm='single',
plotfile='{}P{}_{}_fits.pt'.format(dirn,pointing,l),
output='{}P{}_{}_fits.fits'.format(dirn,pointing,l),
option='fit',
nerrsam=100,
sigma0=0.41,
invgain=0.0)
except Exception as e:
print 'IRAF died:'
print e
pass
return
def dofitprofs(spectrum,specband,varband,redshift,outprefix,alreadyvar=0,startfwhm=4.5,fwhmlim=10,theconstant=10000):
"""
Use IRAF's fitprofs to do spectral line fitting
theconstant is added to the spectrum to prevent negative values that would confuse fitprofs (it should be larger than the most negative value in the spectrum)
"""
outdic={}
##add a constant to the spectrum so that fitprofs won't be confused by negative values
shiftspec='fitprofstempfile.fits';os.system('rm -f '+shiftspec)
iraf.imarith(spectrum,'+',theconstant,shiftspec)
for j in glines.keys():
##redshift the line centers and fitting regions
zbgreg=array(gbgrs[j])*(1+redshift)
zcenters=array(glines[j])*(1+redshift)
##create positions file
os.system('rm -f fitprofs_positions.temp')
for val in zcenters:
os.system('echo '+str(val)+' INDEF INDEF '+str(startfwhm)+' >> fitprofs_positions.temp')
##load spectrum
[waves,spec]=pygetspec(spectrum,specband-1)
[waves,var]=pygetspec(spectrum,varband-1)
if alreadyvar==0:
var=var**2
#find index numbers associated with the bg and fit region and center wavelengths
bg1=0;bg2=0;bg3=0;bg4=0
for i in range(len(waves)):
if (waves[i]>=zbgreg[0]) and (bg1==0): bg1=i
if (waves[i]>=zbgreg[1]) and (bg2==0): bg2=i
if (waves[i]>=zbgreg[2]) and (bg3==0): bg3=i
if (waves[i]>=zbgreg[3]) and (bg4==0): bg4=i
##get estimate of noise parameters
x=append(spec[bg1:bg2],spec[bg3:bg4])+theconstant;y=append(var[bg1:bg2],var[bg3:bg4])+theconstant
slope, intercept, r_value, p_value, std_err=linregress(x,y)
#plt.plot(x,y,'o');plt.plot(x,x*slope+intercept);plt.show();pdb.set_trace()
if intercept<0: intercept=0
noisefloor=intercept+median(x)*slope
##get estimate of background level
bglevel=median(x-theconstant);bgsigma=bglevel/std(x-theconstant)
##run fitprofs
bgstring="med("+str(int(zbgreg[0]))+"-"+str(int(zbgreg[1]))+") med("+str(int(zbgreg[2]))+"-"+str(int(zbgreg[3]))+")"
rgstring=str(int(zbgreg[1]))+' '+str(int(zbgreg[2]))
flog=outprefix+'_fitprofs_log.temp';fplot=outprefix+'_fitprofs'+str(j)+'.gki';os.system('rm -f '+fplot)
try:
iraf.fitprofs(shiftspec,lines=specband,region=rgstring,positions='fitprofs_positions.temp',background=bgstring,profile='gaussian',gfwhm=4,fitbackground='yes',fitpositions='single',fitgfwhm='all',nerrsample=100,sigma0=intercept**.5,invgain=slope,logfile=flog,plotfile=fplot,verbose=0)
except:
print "Fitting failed for "+spectrum+", "+str(glines[j])
os.system("echo '#fitprofs fitting failed' >> "+flog)
for k in range(len(glines[j])):
os.system("echo 'nan nan nan nan nan nan nan' >> "+flog)
##load results
f=open(flog,'r');lst=f.readlines()
for k in range(len(glines[j])):
##did the error calculation work?
if '(' in lst[-1]:
goback=2*(len(glines[j])-k-1);backstep=2
##errors
scenter=float(lst[-1-goback].replace('(','').replace(')','').split()[0])
sflux=float(lst[-1-goback].replace('(','').replace(')','').split()[2])
sew=float(lst[-1-goback].replace('(','').replace(')','').replace('INDEF','nan').split()[3])*(1+theconstant/bglevel) ##correct for theconstant
sfwhm=float(lst[-1-goback].replace('(','').replace(')','').split()[5])
else:
goback=1*(len(glines[j])-k-1);backstep=1
##take the variance floor as the error
scenter=nan
sflux=noisefloor**.5*startfwhm
sfwhm=nan
sew=nan
##values
center=float(lst[-backstep-goback].replace('(','').replace(')','').split()[0])
flux=float(lst[-backstep-goback].replace('(','').replace(')','').split()[2])
ew=float(lst[-backstep-goback].replace('(','').replace(')','').replace('INDEF','nan').split()[3])*(1+theconstant/bglevel)
fwhm=float(lst[-backstep-goback].replace('(','').replace(')','').split()[5])
##reject negative fluxes
##reject objects with too-large FWHM
if flux<0 or fwhm>fwhmlim:
center=nan;flux=nan;fwhm=nan;sflux=nan;scenter=nan;sfwhm=nan
##If continuum was negligable (<2sigma), read out huge equivalent width
if bgsigma<2:
ew=-inf;sEW=-inf
##don't accept a flux error below the noise floor
if sflux<noisefloor**.5*startfwhm: sflux=noisefloor**.5*startfwhm
##save to dictionary
outdic[glines[j][k]]={'cent':center,'scent':scenter,'flux':flux,'sflux':sflux,'fwhm':fwhm,'sfwhm':sfwhm,'EW':ew,'sEW':sew}
###rename lines
outdic2={}
for i in range(len(elines)):
outdic2[linenames[i]]=outdic[elines[i]]
return outdic2