def run_apsum(twodimage,refimage,spectrum,customRun=False):
# this resets the parameters of apextract.apsum
apextract.apsum.unlearn()
apextract.apsum.interactive='no' # non-interactive
apextract.apsum.review='no'
apextract.apsum.background='none'
apextract.apsum.format='multispec'
# apextract.apsum.clean='yes'
# apextract.apsum.weights='variance'
apextract.apsum.nsum=50
apextract.apsum.lsigma=2.0
apextract.apsum.usigma=2.0
# need to specify extraction extension (1, not 0) since there are 2
twodimage = twodimage+'[1]'
# This runs apextract.apsum
apextract.apsum(input=twodimage,output=spectrum,references=refimage)
def run_apsumSci(inputimage,refimage,spectrum,customRun=False):
# this resets the parameters of apextract.apsum
apextract.apsum.unlearn()
apextract.apsum.interactive='no' # non-interactive
apextract.apsum.review='no'
apextract.apsum.background='fit' # we want the background subtracted for science
apextract.apsum.extras = 'yes' # we want the additional spectral bands (sky (3), sigma (4) especially)
apextract.apsum.format='multispec'
apextract.apsum.clean='yes' # we want cosmic rays and bad pixels cleaned for science
apextract.apsum.weights='variance' # we want a weighted extraction for science
apextract.apsum.pfit='fit1d'
apextract.apsum.nsum=-1000 # should deal with bright and faint spectra equally well
apextract.apsum.lsigma=2.0
apextract.apsum.usigma=2.0
# this sets the gain parameter as specified in inputimage's 0-header
hduin = pyfits.open(inputimage[:len(inputimage)-3]) # pyfits open fits file, not fits[1] "file"
hdr = hduin[0].header
thisgain = hdr.get('GAIN',1.0) # default for our usual SALT long-slit spectroscopy settings
hduin.close()
apextract.apsum.gain=thisgain
# This runs apextract.apsum
apextract.apsum(input=inputimage,output=spectrum,references=refimage)
