nord_b = trace_dict['nord_b']
GA_flat = trace_dict['GA_flat']
RO_flat = trace_dict['RO_flat']
Flat = pyfits.getdata(dirout + 'Flat.fits')
RFlat = pyfits.getdata(dirout + 'FlatR.fits')
print '\n\tExtraction of Flat calibration frames:'
Flat_spec_fits = dirout + 'Flat_spec.fits'
Flat_bkg_fits = dirout + 'BKG_flat.fits'
if (os.access(Flat_spec_fits, os.F_OK) == False) or (force_flat_extract):
print "\t\tNo previous Flat extracted or extraction forced, extracting and saving..."
Centers = np.zeros((len(c_all), RFlat.shape[1]))
for i in range(nord):
Centers[i, :] = scipy.polyval(c_all[i, :],
np.arange(len(Centers[i, :])))
BKG = GLOBALutils.get_scat(RFlat, Centers, span=10)
flat_S = GLOBALutils.simple_extraction(RFlat - BKG, c_all, ext_aperture,
min_extract_col, max_extract_col,
npools)
flat_S = GLOBALutils.invert(flat_S)
flat_S = flat_S[::-1]
if (os.access(Flat_spec_fits, os.F_OK)):
os.remove(Flat_spec_fits)
hdu = pyfits.PrimaryHDU(flat_S)
hdu.writeto(Flat_spec_fits)
if (os.access(Flat_bkg_fits, os.F_OK)):
os.remove(Flat_bkg_fits)
hdu = pyfits.PrimaryHDU(BKG)
hdu.writeto(Flat_bkg_fits)
else:
print "\t\tExtracted flat found, loading..."
#print '\t\ty shift = ', pshift, 'pxs'
data = np.dstack((h[1].data, h[2].data)) - MasterBias
centers1 = np.zeros((len(c_all1), data.shape[0]))
centers2 = np.zeros((len(c_all2), data.shape[0]))
for i in range(len(c_all1)):
centers1[i] = np.polyval(c_all1[i], np.arange(data.shape[0]))
for i in range(len(c_all2)):
centers2[i] = np.polyval(c_all2[i], np.arange(data.shape[0]))
print '\t\tEstimating background of scattered light...'
force_bac = False
if (os.access(bac_fits, os.F_OK) == False) or force_bac:
bac1 = GLOBALutils.get_scat(data[:, :, 0].T,
centers1,
span=sky_aperture)
bac2 = GLOBALutils.get_scat(data[:, :, 1].T,
centers2,
span=sky_aperture)
bac = np.dstack((bac1.T, bac2.T))
bach = pyfits.PrimaryHDU(bac)
if os.access(bac_fits, os.F_OK):
os.system('rm ' + bac_fits)
bach.writeto(bac_fits)
else:
bac = pyfits.getdata(bac_fits)
data = data - bac
if (os.access(sky_fits, os.F_OK) == False) or force_bac:
print "\t\tObject name:", obname
print "\t\tDeckr Name = ", h[0].header['DECKNAME']
# Open file, trim, overscan subtract and MasterBias subtract
bac_fits = dirout + 'BAC_' + fsim.split('/')[-1][:-4] + 'spec_' + str(
int(chip)) + '.fits'
data = hiresutils.OverscanTrim(h[chip].data, h[chip].header['DATASEC']).T
c_new, pshift = GLOBALutils.retrace(data, c_all, span=15)
print '\t\ty shift = ', pshift, 'pxs'
centers = np.zeros((len(c_new), nflat.shape[0]))
for i in range(len(c_new)):
centers[i] = np.polyval(c_new[i], np.arange(nflat.shape[0]))
force_bac = False
if (os.access(bac_fits, os.F_OK) == False) or force_bac:
bac = GLOBALutils.get_scat(data, centers, span=10)
bach = pyfits.PrimaryHDU(bac)
if os.access(bac_fits, os.F_OK):
os.system('rm ' + bac_fits)
bach.writeto(bac_fits)
else:
bac = pyfits.getdata(bac_fits)
data = data - bac
data = data / nflat.T
ra = h[0].header['RA'].split(':')
ra = float(ra[0]) + float(ra[1]) / 60. + float(ra[2]) / 3600.
ra = 360. * ra / 24.
dec = h[0].header['DEC'].split(':')
dec = float(dec[0]) + float(dec[1]) / 60. + float(dec[2]) / 3600.
print('\n\tExtraction of Flat calibration frames:')
P_fits = dirout + 'P.fits'
S_flat_fits = dirout +'flat.fits'
S_flat = np.zeros((nord, 3, Flat.shape[1]) )
if ( os.access(P_fits,os.F_OK) == False ) or \
( os.access(S_flat_fits,os.F_OK) == False ) or \
(force_flat_extract):
print("\t\tNo extracted flat object spectra found or extraction forced, extracting and saving...")
Centers = np.zeros((len(c_all),Flat.shape[1]))
for i in range(nord):
Centers[i,:]=scipy.polyval(c_all[i,:],np.arange(len(Centers[i,:])))
bac = GLOBALutils.get_scat(Flat,Centers,span=7)
fl = Flat - bac
#plot(fl[:,1000])
#plot(np.around(Centers[:,1000]).astype('int'),fl[np.around(Centers[:,1000].astype('int')),1000],'ro')
#show()
#print gfd
bacfile = dirout + 'BAC_FLAT.fits'
if (os.access(bacfile,os.F_OK)):
os.remove( bacfile )
hdbac = pyfits.PrimaryHDU( bac )
hdbac.writeto(bacfile)
print("\t\tWill extract",nord,"orders for object fibre...")
P = GLOBALutils.obtain_P(fl,c_all,ext_aperture,RO_fl,\
GA_fl,NSigma_Marsh, S_Marsh, \
N_Marsh, Marsh_alg, min_extract_col,\
h = pyfits.open(dirin + stst)[0]
hth = pyfits.getheader(dirin + stst)
d = h.data
d = pfsutils.OverscanTrim(d, bias_section, over_section)
d -= MasterBias
d /= NorFlat
Centers = np.zeros((len(c_all), d.shape[1]))
for i in range(nord):
Centers[i, :] = scipy.polyval(c_all[i, :],
np.arange(len(Centers[i, :])))
force_bkg = True
bkg_obj_fits = dirout + 'BKG_' + h.header['UT-DATE'] + '_' + h.header[
'UT-TIME'] + '.' + h.header['OBJECT'] + '.fits'
if (os.access(bkg_obj_fits, os.F_OK) == False or force_bkg):
bkg = GLOBALutils.get_scat(d, Centers, span=ext_aperture)
if (os.access(bkg_obj_fits, os.F_OK)):
os.remove(bkg_obj_fits)
hdu = pyfits.PrimaryHDU(bkg)
hdu.writeto(bkg_obj_fits)
else:
bkg = pyfits.getdata(bkg_obj_fits)
d -= bkg
RO, GA = hth['ENOISE'], hth['EGAIN']
P = GLOBALutils.obtain_P(d,c_all,ext_aperture,RO,\
GA,NSigma_Marsh, S_Marsh, \
N_Marsh, Marsh_alg, min_extract_col,\
max_extract_col, npools)
if (os.access(S_flat_fits, os.F_OK) == False) or (os.access(
S_flat_fits_simple,
os.F_OK) == False) or (force_flat_extract) or (os.access(
flat_P, os.F_OK) == False):
print "\t\tNo previous extraction or extraction forced for flat file", "extracting..."
#Flat = utils.invert(Flat)
Flat = pyfits.getdata(dirout + 'MasterFlat.fits')
Flat = Flat.T
if (os.access(bacfile, os.F_OK)) == False or True:
Centers = np.zeros((len(c_all), Flat.shape[0]))
for i in range(c_all.shape[0]):
Centers[i, :] = scipy.polyval(c_all[i, :],
np.arange(len(Centers[i, :])))
bac = GLOBALutils.get_scat(Flat, Centers, span=5)
hdbac = pyfits.PrimaryHDU(bac)
if os.access(bacfile, os.F_OK):
os.system('rm -r ' + bacfile)
hdbac.writeto(bacfile)
Flat -= bac
# Determination the P matrix
if os.access(flat_P, os.F_OK):
P = pyfits.getdata(flat_P)
else:
P = GLOBALutils.obtain_P(Flat,c_all,ext_aperture,roF,\
gaF,NSigma_Marsh, S_Marsh, \
N_Marsh, Marsh_alg, 0,1023, npools)
hdu = pyfits.PrimaryHDU(P)
hdu.writeto(flat_P)
h = pyfits.open(dirin + stst)[0]
ron = h.header['RDNOISE']
gain = h.header['GAIN']
hth = pyfits.getheader(dirin + stst)
d = h.data
d = arcesutils.OverscanTrim(d)
d = arcesutils.bad_col_corr(d)
d -= MasterBias
c_alls = c_all.copy()
Centers = np.zeros((len(c_alls), d.shape[1]))
for i in range(nord):
Centers[i, :] = scipy.polyval(c_alls[i, :],
np.arange(len(Centers[i, :])))
bkg_obj_fits = dirout + 'BKG_' + 'Pref.fits'
if (os.access(bkg_obj_fits, os.F_OK) == False or force_bkg):
bkg = GLOBALutils.get_scat(d, Centers, span=4)
if (os.access(bkg_obj_fits, os.F_OK)):
os.remove(bkg_obj_fits)
hdu = pyfits.PrimaryHDU(bkg)
hdu.writeto(bkg_obj_fits)
else:
bkg = pyfits.getdata(bkg_obj_fits)
d -= bkg
if os.access(Pref_fits, os.F_OK) == False or force_P:
P_ref = np.zeros(d.shape)
for i in range(nord):
P_marsh = GLOBALutils.PCoeff(d, c_alls[i, :], ext_aperture, ron,
gain, NSigma_Marsh, S_Marsh, N_Marsh,
Marsh_alg, min_extract_col,
max_extract_col)
P_ref += P_marsh
MDARKS = trace_dict['DARKS']
dark_times = trace_dict['dtimes']
h = pyfits.open(dirout+'MasterFlat.fits')
Flat = h[0].data
print '\n\tExtraction of Master Flat:'
flat_simple_fits = dirout + 'Flat.spec.simple.fits'
flat_fits = dirout + 'Flat.spec.fits'
P_fits = dirout + 'P.fits'
if ( os.access(flat_simple_fits,os.F_OK) == False ) or ( os.access(flat_fits,os.F_OK) == False ) or force_flat_extract:
Centers = np.zeros((len(c_all),Flat.shape[1]))
for i in range(nord):
Centers[i,:]=scipy.polyval(c_all[i,:],np.arange(len(Centers[i,:])))
bkg = GLOBALutils.get_scat(Flat,Centers,span=15)
Flat -= bkg
flat_simple = GLOBALutils.simple_extraction(Flat,c_all,ext_aperture,min_extract_col,max_extract_col,npools)
P = GLOBALutils.obtain_P(Flat,c_all,ext_aperture,RO_flat,GA_flat,NSigma_Marsh,S_Marsh,N_Marsh,Marsh_alg,min_extract_col,max_extract_col,npools)
flat = GLOBALutils.optimal_extraction(Flat,P,c_all,ext_aperture,RO_flat,GA_flat,S_Marsh,NCosmic_Marsh,min_extract_col,max_extract_col,npools)
flat_simple = flat_simple[::-1]
flat = flat[::-1]
if (os.access(flat_simple_fits,os.F_OK)):
os.remove( flat_simple_fits )
hdu = pyfits.PrimaryHDU( flat_simple )
hdu.writeto( flat_simple_fits )
if (os.access(flat_fits,os.F_OK)):
os.remove( flat_fits )
hdu = pyfits.PrimaryHDU( flat )
hdu.writeto( flat_fits )
if bad_colummn: dat = dupontutils.b_col(dat) dat = dat/Flat c_alls,pshift = GLOBALutils.retrace( dat, c_all ) Centers = np.zeros((len(c_alls),dat.shape[1])) for i in range(nord): Centers[i,:]=scipy.polyval(c_alls[i,:],np.arange(len(Centers[i,:]))) #print 'Scatter Light Determination...' #print 'SN',np.median(dat[Centers[0,1024]:Centers[-1,1024],1024]) if np.median(dat[Centers[0,1024]:Centers[-1,1024],1024])> 0: if ( os.access(bkg_obj_fits,os.F_OK) == False or force_bkg): bkg = GLOBALutils.get_scat(dat,Centers,span=6) if (os.access(bkg_obj_fits,os.F_OK)): os.remove( bkg_obj_fits ) hdu = pyfits.PrimaryHDU( bkg ) hdu.writeto( bkg_obj_fits ) else: bkg = pyfits.getdata(bkg_obj_fits) dat -= bkg else: NCosmic_Marsh = 6 #print 'P matrix determination...' use_ref_P = False if use_ref_P: P = pyfits.getdata(dirout + 'P_ref.fits') Pn = P.copy()