pipered.py

import math
import sys
import os
import numpy as np
from astropy.io import fits as pyfits
from extract_overscan import extract_overscan
from pipeutils import open_fits_file
from functools import partial
from multiprocessing.dummy import Pool as ThreadPool

inlist = str(sys.argv[1])
biasname = str(sys.argv[2])
darkname = str(sys.argv[3])
flatname = str(sys.argv[5])
caldir = str(sys.argv[6])+'/'
outdir = str(sys.argv[7])+'/'
biasname = caldir+biasname
darkname = caldir+darkname
flatname = caldir+flatname

os.system('rm -f '+outdir+'processed.dat')


def reduce_file(filename, bias, dark, flat):
    with open_fits_file(filename) as hdulist:
        overscan = extract_overscan(hdulist)
        data = hdulist[0].data[0:2048,20:2068]
        exposure = hdulist[0].header['exposure']
        corrected = (data-np.median(overscan)-bias-(dark*exposure))/flat
        path, fname = os.path.split(filename)
        outname = outdir+'proc'+fname.replace('.bz2', '')
        print outname
        hdulist[0].data = corrected
        hdulist[0].header.add_history('Overscan of '+str(np.median(overscan))+' subtracted')
        hdulist[0].header.add_history('Bias subtracted using '+str(biasname))
        hdulist[0].header.add_history('Dark subtracted using '+str(darkname))
        hdulist[0].header.add_history('Flat corrected using '+str(flatname))

        command = 'rm -f '+outname
        os.system(command)
        hdulist.writeto(outname)
        dfile = outdir+'processed.dat'
        f = open(dfile, 'a')
        f.write(outname)
        f.close()




def reducer():
    with open_fits_file(biasname) as hdulist:
        bias = hdulist[0].data
    with open_fits_file(darkname) as hdulist:
        dark = hdulist[0].data
    with open_fits_file(flatname) as hdulist:
        flat = hdulist[0].data

    pool = ThreadPool()
    fn = partial(reduce_file, bias=bias, dark=dark, flat=flat)
    with open(inlist) as infile:
        filenames = [line.strip() for line in infile]

    pool.map(fn, filenames)



if __name__ == '__main__':
    reducer()