import os

folderroot = '/Users/lucaizzo/Documents/NOT/test/'

os.chdir(folderroot)

import numpy as np

from astropy.io import fits

from matplotlib import pyplot as plt

import shutil

import sys

from pyraf import iraf

iraf.noao(_doprint=0)

iraf.imred(_doprint=0)

iraf.ccdred(_doprint=0)

iraf.twodspec(_doprint=0)

iraf.longslit(_doprint=0)

iraf.kpnoslit(_doprint=0)

iraf.astutil(_doprint=0)

iraf.onedspec(_doprint=0)

iraf.twodspec.longslit.dispaxis = 2

#read object keywords

for file in os.listdir(os.getcwd()):

if file.endswith('.fits'):

testfile = file

hduo = fits.open(testfile)

#name targets (science & standard)

target = hduo[0].header['OBJECT']

#target2 = 'SP0644p375'

#std = 'SP0305+261'

#create list of science files

sci = []

for file in os.listdir(os.getcwd()):

if file.endswith('.fits'):

sci.append(file+'[1]')

file1 = open('listasci', 'w')

file1.writelines(["%s\n" % item for item in sci])

file1.close()

#copy calib files in the current dir

shutil.copy(folderroot+'bias/bias.fits', folderroot)

shutil.copy(folderroot+'flat/response.fits', folderroot)

#Subtract bias

iraf.imarith('@listasci', '-', 'bias.fits', '@listasci//_2b')

#flat subtraction

iraf.imarith('*_2b.fits', '/', 'response.fits', '@listasci//_2bf')

#SCIENCE

#APALL

iraf.imred.kpnoslit

final = []

for file in os.listdir(os.getcwd()):

if file.endswith('2bf.fits'):

final.append(file)

file1 = open('listafinal', 'w')

file1.writelines(["%s\n" % item for item in final])

file1.close()

f = open('listafinal')

i = 1

for item in f:

file = item.split('\n')[0]

shutil.copy(file, 'spec'+str(i)+'.fits')

i += 1

#FROM NOW -> iraf

iraf.noao.twodspec.apextract

iraf.apall('spec*.fits')

#assign dispersion solution - from now IRAF

shutil.copy('./arc/database/idarc1.ms','./database/.')

for file in os.listdir(os.getcwd()):

if file.endswith('ms.fits'):

iraf.hedit(file,fields="REFSPEC1",value="arc1.ms",add='yes',ver='no',show='yes')

#wavelength calinration

for file in os.listdir(os.getcwd()):

if file.endswith('ms.fits'):

iraf.dispcor(file, 'd'+file)

#flux calibration

shutil.copy('./stds/sens.0001.fits','.')

shutil.copy('./stds/lapalmaextinct.dat','.')

for file in os.listdir(os.getcwd()):

if file.startswith('dspec'):

iraf.calibrate(file, 'f'+file)

#combine spectra

finalcomb = []

for file in os.listdir(os.getcwd()):

if file.startswith('fds'):

finalcomb.append(file)

file1 = open('listascombine', 'w')

file1.writelines(["%s\n" % item for item in finalcomb])

file1.close()

iraf.scombine('@listascombine', 'temp_quick.fits')

iraf.scopy('temp_quick.fits',target+'_quick.fits',w1='4000',w2='9000')

#mv final file in a dedicated folder

shutil.copy(target+'_quick.fits','./output/.')

#remove temp FILES

os.remove('lapalmaextinct.dat')

for file in os.listdir(os.getcwd()):

if file.endswith('fits'):

os.remove(file)

elif file.startswith('lista'):

os.remove(file)

elif file.startswith('log'):

os.remove(file)

shutil.rmtree('database')