for i in range(len(input_y)):

if input_y[i] == min(input_y):

minpos = input_x[i]

# fitfunc = lambda p, x: abs(p[0])*(x-p[1])**2 + p[2] # Target function

# errfunc = lambda p, x, y: fitfunc(p, x) - y # Distance to the target function

# p0 = [1,1.0,0] # Initial guess for the parameters

# p1, success = optimize.leastsq(errfunc, p0[:], args=(input_x,input_y))

# print p1[1]

# #plt.plot(input_x,abs(p1[0])*(input_x-p1[1])**2 + p1[2])

# if abs(p1[1] - minpos) < 0.1:

# minpos = p1[1]

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",2000,check=1,exact=1)

os.system("rm fxcor_shift*")

iraf.fxcor(

objects = input_file, \

templates = input_rv, \

apertures = "*", \

cursor = "",\

continuum = "both",\

filter = "both",\

rebin = "smallest",\

pixcorr = 0,\

osample = lines,\

rsample = lines,\

apodize = 0.2,\

function = "gaussian",\

width = 15,\

height= 0.,\

peak = 0,\

minwidth = 15,\

maxwidth = 15,\

weights = 1.,\

background = "INDEF",\

window = "INDEF",\

wincenter = "INDEF",\

output = "fxcor_shift",\

verbose = "long",\

imupdate = 0,\

graphics = "stdgraph",\

interactive = 0,\

autowrite = 1,\

ccftype = "image",\

observatory = "sso",\

continpars = "",\

filtpars = "",\

keywpars = "")

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

vel_shift = functions.read_table(vel_shift)

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

if vel_shift == "INDEF":

vel_shift = 0

print "shifting by ",vel_shift,"km/s"

telluric_region = eval("TELLURIC_REGION_"+molecule)

telluric_region_list = string.split(telluric_region,",")

for n in range(len(telluric_region_list)):

region = telluric_region_list[n][1:]

region = string.split(region,"-")

temp = []

for i in region:

temp.append(float(i))

telluric_region_list[n] = temp

### Copy telluric line spectra to working directory

telluric_fits = grating + "_"+molecule+".fits"

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

os.system("rm temp_norm*")

os.system("rm temp_spec*")

os.system("cp -f "+spec_name+" temp_spec.fits")

iraf.continuum(

input = spec_name,\

output = "temp_norm.fits",\

lines = "*",\

bands = "*",\

type = "ratio",\

replace = 0,\

wavescale = 1,\

logscale = 0,\

override = 1,\

listonly = 0,\

logfiles = "logfile",\

interactive = 0,\

sample = "*",\

naverage = 1,\

function = "spline3",\

order = 20,\

low_reject = 2.0,\

high_reject = 5.0,\

niterate = 5,\

grow = 2.0,\

ask = "yes")

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

### Find shift ###

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

shift = run_fxcor("telluric.fits","temp_norm.fits",telluric_region)

os.system("rm telluric.dat")

iraf.dopcor(

input = "telluric.fits",\

output = "telluric.fits",\

redshift = shift,\

isvelocity = 1,\

add = 1,\

dispersion = 1,\

flux = 0,\

verbose = 0)

iraf.wspectext(

input = "telluric.fits",\

output = "telluric.dat",\

header = 0)

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

### Iterative telluric subtraction ###

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

def iterate():

os.system("rm temp_norm.dat")

iraf.wspectext(

input = "temp_norm.fits",\

output = "temp_norm.dat",\

header = 0)

data_spec = transpose(loadtxt("temp_norm.dat"))

wave = arange(min(data_spec[0]),max(data_spec[0]),1)

data_flux = interpolate.splrep(data_spec[0],data_spec[1])

data_flux = interpolate.splev(wave,data_flux)

telluric_spec = transpose(loadtxt("telluric.dat"))

telluric_flux = interpolate.splrep(telluric_spec[0],telluric_spec[1])

telluric_flux = interpolate.splev(wave,telluric_flux)

### Loop through telluric scaling

telluric_scaling = []

rms_list = []

maxscale = 1.08

for scale in arange(0.0,maxscale,0.01):

scatter_list = []

for region in telluric_region_list:

temp_flux = []

temp_tel = []

for i in range(len(wave)):

if wave[i] > region[0] and wave[i] < region[1]:

temp_flux.append(data_flux[i])

temp_tel.append(telluric_flux[i])

if wave[i] > region[1]:

break

temp_flux = array(temp_flux)

temp_tel = array(temp_tel)

scatter = temp_flux / (temp_tel * scale + (1-scale))

# plt.plot(scatter)

# plt.show()

scatter_list.append(std(scatter))

telluric_scaling.append(scale)

rms_list.append(average(scatter_list))

telluric_scaling,rms_list = array(telluric_scaling),array(rms_list)

best_scale = find_min(telluric_scaling,rms_list)

if best_scale > maxscale:

best_scale = maxscale

if best_scale < 0:

best_scale = 0

print "scaling telluric by",best_scale

# plt.plot(telluric_scaling,rms_list)

# plt.show()

os.system("cp telluric.fits telluric_temp.fits")

iraf.sarith(

input1 = "telluric_temp.fits",\

op = "*",\

input2 = best_scale,\

output = "telluric_temp.fits",\

w1 = "INDEF",\

w2 = "INDEF",\

apertures = "",\

bands = "",\

beams = "",\

apmodulus = 0,\

reverse = 0,\

ignoreaps = 1,\

format = "multispec",\

renumber = 0,\

offset = 0,\

clobber = 1,\

merge = 0,\

rebin = 0,\

verbose = 0)

iraf.sarith(

input1 = "telluric_temp.fits",\

op = "+",\

input2 = 1-best_scale,\

output = "telluric_temp.fits",\

w1 = "INDEF",\

w2 = "INDEF",\

apertures = "",\

bands = "",\

beams = "",\

apmodulus = 0,\

reverse = 0,\

ignoreaps = 1,\

format = "multispec",\

renumber = 0,\

offset = 0,\

clobber = 1,\

merge = 0,\

rebin = 0,\

verbose = 0)

iraf.sarith(

input1 = "temp_spec.fits",\

op = "/",\

input2 = "telluric_temp.fits",\

output = "temp_spec",\

w1 = "INDEF",\

w2 = "INDEF",\

apertures = "",\

bands = "",\

beams = "",\

apmodulus = 0,\

reverse = 0,\

ignoreaps = 1,\

format = "multispec",\

renumber = 0,\

offset = 0,\

clobber = 1,\

merge = 0,\

rebin = 0,\

verbose = 0)

iraf.sarith(

input1 = "temp_norm.fits",\

op = "/",\

input2 = "telluric_temp.fits",\

output = "temp_norm",\

w1 = "INDEF",\

w2 = "INDEF",\

apertures = "",\

bands = "",\

beams = "",\

apmodulus = 0,\

reverse = 0,\

ignoreaps = 1,\

format = "multispec",\

renumber = 0,\

offset = 0,\

clobber = 1,\

merge = 0,\

rebin = 0,\

verbose = 0)

return best_scale

best_scaling = 1.0

while best_scaling > 0.05:

best_scaling = iterate()