#!/usr/bin/env python

'''

call: daoproc_v2

purpose: This script is using IRAF packages in Pyraf to perform aperture

protometry in astronomical *.fits images.

inputs: image.fits, telescope/CCD parameters (gain,read-out-noise)

FWHM of the source.

outputs: it first generates a PSF image using a statistically

significant sample of stars. It then creates files containing

the detections/photometry.

Version: v2 - G. Maravelias, T. Bitsakis

'''

import os, sys, shutil, math, time

from pyraf import iraf

from iraf import noao, digiphot, daophot

# ==================================================

# PARAMETERS TO BE SET:

# ==================================================

# not known exactly ...

gain = 6.61 # Individual gain in e/ADU

rdnoise = 0.76 # Read noise in e/px (/read)

Nimages = 1 # Number of images used

N_loops = 4 # Number of loops to execute

# fwhm = 2.50 # FWHM of a star in the image

fwhm = input('Enter FWHM: ')

maxpsfstars = 150 # Number of stars in psf model

sigmabgr = 3. # Background sigma

datamin = 1. # Min(sky)-5*sigmabgr

datamax = 28000. # Maxdata

threshold = 2. # Detection threshold

# ==================================================

ans = raw_input('Remove previous files (y/n): ')

if ans == 'y':

os.system('rm *sub.*')

os.system('rm *pst.*')

os.system('rm *final.*')

os.system('rm *grf.*')

# os.system('rm *psf.*')

# os.system('rm *image_of_psf.*')

# ==================================================

# FUNCTION

def transform(infile,outfile):

print "\nTrasnformation completed!"

# INPUT FILE

if len(sys.argv)!=2:

sys.exit('ERROR: please provide a file')

flnm, flext = os.path.splitext(sys.argv[1])

# setting parameters

iraf.daofind.unlearn

iraf.phot.unlearn

iraf.allstar.unlearn

iraf.datapars.unlearn

iraf.daopars.unlearn

iraf.findpars.unlearn

iraf.centerpars.unlearn

iraf.fitskypars.unlearn

# EDIT PARAMETERS HERE >>>

iraf.datapars.setParam('fwhmpsf',fwhm)

iraf.datapars.setParam('sigma',sigmabgr)

iraf.datapars.setParam('datamin',datamin)

iraf.datapars.setParam('datamax',datamax)

# this is not probably correct ...

iraf.datapars.setParam('readnoise',math.sqrt(Nimages)*rdnoise)

iraf.datapars.setParam('epadu',gain*Nimages)

iraf.datapars.setParam('itime','270') # 4 to 5 min

iraf.findpars.setParam('threshold',threshold) # detection threshold in sigma above background

iraf.centerpars.setParam('calgori','none')

iraf.centerpars.setParam('cbox',2*fwhm)

iraf.fitskypars.setParam('salgori','mode')

iraf.fitskypars.setParam('annulus',4*fwhm)

iraf.fitskypars.setParam('dannulu',4*fwhm)

iraf.photpars.setParam('apertur',1*fwhm)

iraf.daopars.setParam('function','auto')

iraf.daopars.setParam('varorder','2')

iraf.daopars.setParam('psfrad',4*fwhm+1)

iraf.daopars.setParam('fitrad',1*fwhm)

iraf.daopars.setParam('sannulus',4*fwhm)

iraf.daopars.setParam('wsannulus',4*fwhm)

times_start = time.ctime()

times_start_float = time.time()

times = {}

if os.path.exists(flnm+'.sub.0'+flext):

pass

else:

shutil.copy(flnm+flext,flnm+'.sub.0'+flext) # formatting reasons only

for i in range(N_loops):

#for i in range(2):

initimg = flnm+'.sub.0.fits'

runnm = flnm+'.sub.'+str(i)

print "\n>>> Working on",runnm+'.fits',"<<<\n"

print "========================================="

print "...running daofind for", runnm+".fits"

print "========================================="

tds = time.time()

if os.path.exists(runnm+'.coo'):

print " File found! skipping this step"

pass

else:

iraf.daofind(image=runnm+'.fits',output=runnm+'.coo', verify='no')

tde = time.time()

times[runnm+'_daofind']=tde-tds

print "========================================="

print "...running phot for", runnm+".coo"

print "========================================="

tps = time.time()

if os.path.exists(runnm+'.mag'):

print " File found! skipping this step"

pass

else:

iraf.phot(image=runnm+'.fits',coords=runnm+'.coo',output=runnm+'.mag', verify='no') # on subtracted image

tpe = time.time()

times[runnm+'_phot']=tpe-tps

# check for psf.fits image and prompt to create if does not exist - only for sub.0

if not os.path.exists(flnm+'.psf.fits'):

print " "

print "========================================="

print "...creating psf"

print "========================================="

print " 1. Select stars to keep by pressing 'a' or 'd' to delete them."

print " 2. After the selection is finished, select the ds9 window and press 'w' to force the use of these stars for psf creation."

print " 3. To quit press 'q' at the ds9 window and again 'q' at the terminal. The program will go on automatically without any human interaction."

print " (Hint: you can safely leave office for a beer or coffee.)"

raw_input('Ready ? ("enter" to continue)')

iraf.pstselect(image=flnm+'.sub.0.fits',photfile=runnm+".mag",pstfile=flnm+".pst.1",maxnpsf=maxpsfstars,verify="no")

pstregfl = open(flnm+".pst.1.reg",'w')

pstregfl.write('global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=0 delete=1 include=1 source=1\nphysical\n')

pstfl = open(flnm+".pst.1",'r')

pstlns = pstfl.readlines()

pstfl.close()

for s in range(65,len(pstlns),1):

prts = pstlns[s].split()

star_id = prts[0]

xpos = prts[1]

ypos = prts[2]

#print star_id, xpos, ypos

pstregfl.write('point('+str(xpos)+','+str(ypos)+') # point=cross text={'+star_id+'}\n')

pstregfl.close()

os.system("/usr/local/bin//ds9 "+flnm+'.sub.0.fits'+" -regions "+flnm+".pst.1.reg"+" &")

tfs = time.time()

iraf.psf(image=flnm+'.sub.0.fits',photfile=flnm+'.sub.0.mag',pstfile=flnm+'.pst.1',psfimage=flnm+'.psf.fits',

opstfile=flnm+'.pst.2',groupfile=flnm+'.grf.psg',interactive="no",showplots="no",verify="no")

tfe = time.time()

times[runnm+'_psf']=tfe-tfs

iraf.seepsf(psfimage=flnm+'.psf.fits', image=flnm+'.image_of_psf.fits')

if i==0:

shutil.copy(runnm+'.mag',runnm+'.tot.mag') # formatting reasons only

else:

print "========================================="

print "...merging phot lists"

print "========================================="

iraf.pfmerge(inphotfi=str(flnm+'.sub.'+str(i-1)+'.als'+','+runnm+'.mag'),outphotf=runnm+'.tot.mag')

iraf.prenumber(runnm+'.tot.mag')

print "========================================="

print "...running allstar for", runnm+'.fits'

print "========================================="

iraf.daopars.setParam('recenter','yes')

tas = time.time()

iraf.allstar(image=initimg,photfile=runnm+'.tot.mag',psfimage=flnm+'.psf.fits',allstarf=runnm+'.als',rejfile=runnm+'.arj',subimage=flnm+'.sub.'+str(i+1)+'.fits',cache='no',verify='no') # ALLSTAR on original sub.0

tae = time.time()

times[runnm+'_allstar']=tae-tas

# removing the merged phot file (not needed for analysis)

os.remove(runnm+'.tot.mag')

print "\n>>> END OF DAOLOOP #"+str(i)

# Creating the total list of positions for all stars (after running allstar) for input in other routines (e.g. Ha photometry)

transform(str(runnm)+".als",str(flnm)+".final.list.coo")

# Printing parameters to check

print "\n\nChecking the persistence of parameters:"

print "fwhm:", iraf.datapars.getParam('fwhmpsf')

print "sigma", iraf.datapars.getParam('sigma')

print "datamin:", iraf.datapars.getParam("datamin")

print "datamax:", iraf.datapars.getParam("datamax")

print "effective gain:", iraf.datapars.getParam('epadu')

print "effective readnoise", iraf.datapars.getParam('readnoise')

print "exposure time:", iraf.datapars.getParam("itime")

print "cbox dimension:", iraf.centerpars.getParam('cbox')

print "psfrad:", iraf.daopars.getParam("psfrad")

print "fitrad:", iraf.daopars.getParam("fitrad")

print "detection threshold:", iraf.findpars.getParam("threshold")

print "phot sky annulus:", iraf.fitskypars.getParam("annulus")

print "psf sky annulus:", iraf.daopars.getParam("sannulus")

print "phot aperture:", iraf.photpars.getParam('apertur')

print "\nTimings, starting on", times_start

for k in sorted(times.iterkeys()):

print k, ':', "{0:.2f}".format(times[k]), 's'

print "...finishing on", time.ctime(), "-- running for:", "{0:.3f}".format((time.time()-times_start_float)/3600.),"h"

# Removing extra files no needed

for i in range(N_loops-1):

os.system('rm *sub.'+str(i)+'.*')

print "\nThe DaoProcess has been executed!"