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
if (os.access(Pref_fits, os.F_OK)):
os.remove(Pref_fits)
hdu = pyfits.PrimaryHDU(P_ref)
hdu.writeto(Pref_fits)
else:
print "\tWeights for optimal extraction loaded..."
P_ref = pyfits.getdata(Pref_fits)
# Extract Flat
print '\n\tExtraction of Flat calibration frames:'
Flat_spec_fits = dirout + 'Flat_spec.fits'
P_fits = dirout + 'P_flat.fits'
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
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..."
for i in range(nord):
P_marsh = GLOBALutils.PCoeff( fl, c_all[i,:], ext_aperture, RO_fl, GA_fl,\
NSigma_Marsh, S_Marsh, N_Marsh, Marsh_alg, min_extract_col,max_extract_col )
P += P_marsh
if (os.access(P_fits,os.F_OK)):
os.remove( P_fits )
hdu = pyfits.PrimaryHDU( P )
hdu.writeto( P_fits )
S_flat = GLOBALutils.optimal_extraction(fl,P,c_all,ext_aperture,RO_fl,GA_fl,\
S_Marsh,10*NCosmic_Marsh,min_extract_col,max_extract_col,npools)
for i in range(nord):
S_flat[i,1] = S_flat[i,1][::-1]
S_flat[i,2] = S_flat[i,2][::-1]
if (os.access(S_flat_fits,os.F_OK)):
os.remove( S_flat_fits )
Flat = MasterFlat.T #- bac
Centers = np.zeros((nord_ob, MasterFlat.shape[0]))
ejx = np.arange(MasterFlat.shape[0])
imshow(Flat, vmin=0, vmax=10000)
for i in range(nord_ob):
Centers[i, :] = scipy.polyval(c_ob[i], ejx)
plot(ejx, Centers[i, :], 'r')
show()
#bac = FIDEOSutils.scat_flat(MasterFlat.T,c_ob,c_co)
for i in range(nord_ob):
print i
try:
P_marsh = GLOBALutils.PCoeff( Flat, c_ob[i,:], ext_aperture_ob, RO_ob, GA_ob,\
NSigma_Marsh, S_Marsh, N_Marsh, Marsh_alg ,\
min_extract_col,max_extract_col )
P_ob += P_marsh
except:
print 'problem'
i += 1
S_flat_ob_simple = GLOBALutils.simple_extraction(Flat,c_ob,ext_aperture_ob,min_extract_col,\
max_extract_col,npools)
S_flat_ob = GLOBALutils.optimal_extraction(Flat,P_ob,c_ob,ext_aperture_ob,RO_ob,GA_ob,S_Marsh,\
NCosmic_Marsh,min_extract_col,max_extract_col,npools)
S_flat_ob_simple = GLOBALutils.invert(S_flat_ob_simple)
S_flat_ob = GLOBALutils.invert(S_flat_ob)
if (os.access(P_ob_fits, os.F_OK)):