### Load python modules

from pyraf import iraf

from numpy import *

import string

import sys

import os

import pyfits

### Load functions script (located in the same folder)

import functions

### Load iraf moduels

iraf.noao()

iraf.imred()

iraf.imred.ccdred()

iraf.imred.kpnoslit()

iraf.noao.rv()

iraf.astutil()

###################

### Description ###

###################

### For accurate RV measurements, the telluric lines can be another

### way to calibrate our stellar spectrum. The telluric lines are stable

### to 10m/s over a long period, so they can provide a first order

### shift calibration that can be applied to the spectrum.

### We cross correlate the Oxygen telluric lines against an UVES spectrum

### of the same region, and apply the shift correction.

### HOWEVER, since the telluric lines are not in the same region as the

### stellar lines used for RV CC, this helps but does not correct everything.

### usage: telluric_correction.py file_path file_name

#################

### Functions ###

#################

def run_fxcor(input_file,input_rv,lines,output,fitshead_update,npoints,functiontype):

keywpars = "")

########################

### Start of program ###

########################

### Set file_path

file_path = sys.argv[1]

file_path_temp = file_path + "temp/"

file_path_reduced = file_path + "reduced/"

file_name = sys.argv[2]

hdulist = pyfits.open(file_path + file_name)

object_mjd = hdulist[0].header['MJD-OBS']

hdulist.close()

camera = functions.read_config_file("CAMERA")

grating = functions.read_config_file("GRATING")

dichroic = functions.read_config_file("DICHROIC")

telluric_region = functions.read_param_file("TELLURIC_REGION")

### Copy telluric line spectra to working directory

telluric_fits = grating + "_telluric.fits"

os.system("cp -f telluric_fits/" + telluric_fits + " " + file_path_temp+"telluric.fits")

### Get slice numbers

image_slices = functions.read_ascii(file_path_temp + "stellar_apertures.txt")

### We want to change directory to ../temp/

### This is because of some stupid way autoidentify names database files

program_dir = os.getcwd() + "/" #Save the current working directory

os.chdir(file_path_temp) #Change to ../temp/ dir

##################

### Find shift ###

##################

for im_slice in image_slices:

print "CC with telluric for wavelength calibration"

os.system("rm apshift*")

good_correction = False

no_trials = 0

npoints = 20

while (not good_correction) and no_trials < 5:

os.system("rm apshift*")

### Makesure keywpars is set at default

iraf.unlearn(iraf.keywpars)

iraf.filtpars.setParam("f_type","square",check=1,exact=1)

iraf.filtpars.setParam("cuton",50,check=1,exact=1)

iraf.filtpars.setParam("cutoff",10000,check=1,exact=1)

run_fxcor("norm_" + im_slice + "_" + file_name,"telluric.fits",telluric_region,"apshift",0,npoints,"gaussian")

vel_shift = functions.read_ascii("apshift.txt")

vel_shift = functions.read_table(vel_shift)

vel_shift = str(vel_shift[0][11])

if not vel_shift == "INDEF":

good_correction = True

else:

print "Fit did not converge, trying again with ",npoints,"n_points"

npoints = npoints + 10

no_trials = no_trials + 1

### IF it still doesn't work, use a the centre1d function

if vel_shift == "INDEF":

os.system("rm apshift*")

### Makesure keywpars is set at default

iraf.unlearn(iraf.keywpars)

iraf.filtpars.setParam("f_type","square",check=1,exact=1)

iraf.filtpars.setParam("cuton",50,check=1,exact=1)

iraf.filtpars.setParam("cutoff",10000,check=1,exact=1)

run_fxcor("norm_" + im_slice + "_" + file_name,"telluric.fits",telluric_region,"apshift",0,20,"center1d")

vel_shift = functions.read_ascii("apshift.txt")

vel_shift = functions.read_table(vel_shift)

vel_shift = str(vel_shift[0][11])

print "Applying pixel shift of (km/s)"

print vel_shift

### If it is STILL not working, use vshift = 0km/s

if vel_shift == "INDEF":

vel_shift = 0.0

if float(vel_shift) > 30:

vel_shift = 0.0

###################

### Apply shift ###

###################

os.system("rm temp.fits")

iraf.dopcor(

input = "norm_" + im_slice + "_" + file_name,\

output = "temp.fits",\

redshift = vel_shift,\

isvelocity = 1,\

add = 1,\

dispersion = 1,\

flux = 0,\

apertures = "*",\

verbose = 1)

os.system("rm norm_" + im_slice + "_" + file_name)

os.system("mv temp.fits norm_" + im_slice + "_" + file_name)