torder = 0
for order in range(ro0,ro0+n_useful+1,1):
#print order
order_s = str(order)
if (order < 100):
order_s = '0' + str(order)
thar_order_orig = lines_thar[order - difo]
#IV = iv_thar_ob_R[order,:]
L = np.where(thar_order_orig != 0)[0]
IV = 1. / (thar_order_orig / gain + (ron/gain)**2 )
IV[L] = 0.
wei = np.sqrt( IV )
thar_order = thar_order_orig #- bkg
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths, rms_ms, residuals, centroids,sigmas, intensities \
= GLOBALutils.Initial_Wav_Calibration( order_dir+'order_'+order_s+'.iwdat', thar_order, order, np.ones(len(thar_order)), rmsmax=300, minlines=10, FixEnds=False,Dump_Argon=dumpargon, Dump_AllLines=True, Cheby=use_cheby,porder=3,rough_shift=rough_shift)
if (order == int(.5*n_useful)+ro0):
if (use_cheby):
Global_ZP = GLOBALutils.Cheby_eval( coeffs_pix2wav, 0.5*len(thar_order), len(thar_order) )
else:
Global_ZP = scipy.polyval( coeffs_pix2wav, 0.0 )
All_Pixel_Centers = np.append( All_Pixel_Centers, pixel_centers )
All_Wavelengths = np.append( All_Wavelengths, wavelengths )
All_Orders = np.append( All_Orders, np.zeros( len(pixel_centers) ) + order -ro0)
All_Centroids = np.append( All_Centroids, centroids)
All_Sigmas = np.append( All_Sigmas, sigmas)
All_Intensities = np.append( All_Intensities, intensities )
All_residuals = np.append( All_residuals, residuals )
order_s = '0' + str(order)
thar_order_orig = lines_thar2[order]
I = np.where(np.isnan(thar_order_orig))
J = np.where(np.isnan(thar_order_orig) == False)
thar_order_orig[I] = np.median(thar_order_orig[J])
thar_order = thar_order_orig - scipy.signal.medfilt(
thar_order_orig, 101)
wei = np.ones(len(thar_order))
if order == 0:
do_xc = False
else:
do_xc = True
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths,\
rms_ms, residuals, centroids, sigmas, intensities =\
GLOBALutils.Initial_Wav_Calibration(order_dir+'nborder_'+\
order_s+'.iwdat', thar_order, order, wei, rmsmax=100, \
minlines=20,FixEnds=False,Dump_Argon=dumpargon,sigmai=2.,\
Dump_AllLines=True, Cheby=use_cheby,porder=ncoef_x,do_xc=False, line_width=6,pixelization=True)
if order == 7:
Global_ZP = GLOBALutils.Cheby_eval(coeffs_pix2wav,
0.5 * (len(thar_order) - 1),
len(thar_order))
All_Pixel_Centers = np.append(All_Pixel_Centers, pixel_centers)
All_Wavelengths = np.append(All_Wavelengths, wavelengths)
All_Orders = np.append(All_Orders,
np.zeros(len(pixel_centers)) + order)
All_Centroids = np.append(All_Centroids, centroids)
All_Sigmas = np.append(All_Sigmas, sigmas)
All_Intensities = np.append(All_Intensities, intensities)
for order in range(n_useful):
order_s = str(order)
if (order < 10):
order_s = '0' + str(order)
thar_order_orig = lines_thar[order, :]
IV = iv_thar[order, :]
wei = np.sqrt(IV)
#bkg = PFSutils.Lines_mBack(thar_order_orig, IV, thres_rel=3)
#thar_order = thar_order_orig - bkg
thar_order = thar_order_orig
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths,\
rms_ms, residuals, centroids, sigmas, intensities =\
GLOBALutils.Initial_Wav_Calibration(order_dir+'norder_'+\
order_s+'o.iwdat', thar_order, order, wei, rmsmax=100, \
minlines=10,FixEnds=False,Dump_Argon=dumpargon,\
Dump_AllLines=True, Cheby=use_cheby,porder=ncoef_x,fact=fact,del_width=30.)
if (order == 32):
if (use_cheby):
Global_ZP = GLOBALutils.Cheby_eval(coeffs_pix2wav,
0.5 * len(thar_order),
len(thar_order))
else:
Global_ZP = scipy.polyval(coeffs_pix2wav, 0.0)
All_Pixel_Centers = np.append(All_Pixel_Centers, pixel_centers)
All_Wavelengths = np.append(All_Wavelengths, wavelengths)
All_Orders = np.append(All_Orders,
np.zeros(len(pixel_centers)) + order)
All_Centroids = np.append(All_Centroids, centroids)
for order in range(len(c_all)):
order_s = str(order)
if (order < 10):
order_s = '0' + str(order)
thar_order_orig = lines_thar[order]
I = np.where(np.isnan(thar_order_orig))
J = np.where(np.isnan(thar_order_orig) == False)
thar_order_orig[I] = np.median(thar_order_orig[J])
thar_order = thar_order_orig - scipy.signal.medfilt(
thar_order_orig, 101)
wei = np.ones(len(thar_order))
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths,\
rms_ms, residuals, centroids, sigmas, intensities =\
GLOBALutils.Initial_Wav_Calibration(order_dir+'echorder_'+\
order_s+'_'+str(int(chip))+'.iwdat', thar_order, order, wei, rmsmax=100, \
minlines=20,FixEnds=False,Dump_Argon=dumpargon,\
Dump_AllLines=True, Cheby=use_cheby,porder=ncoef_x)
if (chip == 2) and (order == 8):
Global_ZP = GLOBALutils.Cheby_eval(coeffs_pix2wav,
0.5 * (len(thar_order) - 1),
len(thar_order))
All_Pixel_Centers = np.append(All_Pixel_Centers, pixel_centers)
All_Wavelengths = np.append(All_Wavelengths, wavelengths)
All_Orders = np.append(All_Orders,
np.zeros(len(pixel_centers)) + order)
All_Centroids = np.append(All_Centroids, centroids)
All_Sigmas = np.append(All_Sigmas, sigmas)
All_Intensities = np.append(All_Intensities, intensities)
if (order < 10):
order_s = '0' + str(order)
thar_order_orig = lines_thar[order, :]
#bkg = PFSutils.Lines_mBack(thar_order_orig, IV, thres_rel=3)
thar_order = thar_order_orig - scipy.signal.medfilt(
thar_order_orig, 21)
wei = np.ones(len(thar_order))
ccf_max, rshift = GLOBALutils.cor_thar(lines_thar[order],filename=order_dir+'order_'+\
order_s+'.iwdat',span=20,binning=binx)
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths,\
rms_ms, residuals, centroids, sigmas, intensities =\
GLOBALutils.Initial_Wav_Calibration(order_dir+'order_'+\
order_s+'.iwdat', thar_order, order, wei, rmsmax=100, \
minlines=30,FixEnds=False,Dump_Argon=dumpargon,\
Dump_AllLines=True, Cheby=use_cheby,porder=5,del_width=4.0,\
binning=binx,rough_shift=rshift,line_width=6)
fwhms_lns = sigmas * 2.355
inis_lns = pixel_centers - fwhms_lns * 0.5
fins_lns = pixel_centers + fwhms_lns * 0.5
inis_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav, inis_lns,
float(len(thar_order)))
fins_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav, fins_lns,
float(len(thar_order)))
fwhms_wvs = fins_wvs - inis_wvs
resolution = wavelengths / fwhms_wvs
#print "\t\t\tmedian Resolution of order", order, '('+str(np.around(np.median(wavelengths)))+' A)=', np.around(np.median(resolution))
#plot(wavelengths, resolution,'ro')
trans = np.zeros([nup, 4])
while orre <= or40:
order_s = str(order)
if (order < 10):
order_s = '0' + str(order)
thar_order_orig = lines_thar[orre, :]
IV = iv_thar[orre, :]
wei = np.sqrt(IV)
#bkg = utils.Lines_mBack(thar_order_orig, IV, thres_rel=3)
#thar_order = thar_order_orig - bkg
thar_order = thar_order_orig
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths,\
rms_ms, residuals, centroids, sigmas, intensities \
= GLOBALutils.Initial_Wav_Calibration(order_dir+'gorder'+order_s+'.dat',\
thar_order,order,wei,rmsmax=5000000,\
minlines=6,FixEnds=True,Dump_Argon=False,\
Dump_AllLines=True, Cheby=use_cheby,rough_shift=delta)
if (order == 20):
if (use_cheby):
Global_ZP = GLOBALutils.Cheby_eval(coeffs_pix2wav, 511,
len(thar_order))
else:
Global_ZP = scipy.polyval(coeffs_pix2wav, 0.0)
#print residuals
All_Pixel_Centers = np.append(All_Pixel_Centers, pixel_centers)
All_Wavelengths = np.append(All_Wavelengths, wavelengths)
All_Orders = np.append(All_Orders,
np.zeros(len(pixel_centers)) + order)
All_Centroids = np.append(All_Centroids, centroids)
All_Sigmas = np.append(All_Sigmas, sigmas)
for order in range(orderi,orderf+1):
order_s = str(order)
if (order < 10):
order_s = '0'+str(order)
thar_order_orig = lines_thar[order,:]
IV = iv_thar[order,:]
wei = np.sqrt( IV )
bkg = scipy.signal.medfilt(thar_order_orig,201)
thar_order = thar_order_orig - thar_order_orig.min()
f = open(order_dir+'order_'+order_s+sufix)
lines = f.readlines()
if len(lines)>5:
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths, rms_ms,\
residuals, centroids, sigmas, intensities = GLOBALutils.Initial_Wav_Calibration( \
order_dir+'order_'+order_s+sufix, thar_order, order, wei,\
rmsmax=200, minlines=10, FixEnds=False, Dump_Argon=False, \
Dump_AllLines=True, Cheby=use_cheby, rough_shift=rough_shift,do_xc=False)
"""
fwhms_lns = sigmas*2.355
inis_lns = pixel_centers - fwhms_lns*0.5
fins_lns = pixel_centers + fwhms_lns*0.5
inis_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav,inis_lns,float(len(thar_order)))
fins_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav,fins_lns,float(len(thar_order)))
fwhms_wvs = inis_wvs - fins_wvs
resolution2 = wavelengths / fwhms_wvs
print "\t\t\tmedian Resolution of order", order, '=', np.around(np.median(resolution2))
#"""
if (order == int(0.5*n_useful)):
if (use_cheby):
Global_ZP = GLOBALutils.Cheby_eval( coeffs_pix2wav, 0.5*len(thar_order), len(thar_order) )
OK = []
OW = []
while order < n_last:
order_s = str(order)
if (order < 10):
order_s = '0'+str(order)
thar_order_orig = lines_thar[orre,:]
IV = iv_thar[orre,:]
wei = np.sqrt( IV )
bkg = GLOBALutils.Lines_mBack(thar_order_orig, IV, thres_rel=3, line_w=10)
thar_order = thar_order_orig - bkg
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths, rms_ms,\
residuals, centroids, sigmas, intensities = GLOBALutils.Initial_Wav_Calibration( \
order_dir+'order_'+order_s+'o.iwdat', thar_order, order, wei, rmsmax=1000, \
minlines=10, FixEnds=False, Dump_Argon=False, Dump_AllLines=True, Cheby=use_cheby, \
rough_shift = rough_shift)
fwhms_lns = sigmas*2.355
inis_lns = pixel_centers - fwhms_lns*0.5
fins_lns = pixel_centers + fwhms_lns*0.5
inis_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav,inis_lns,float(len(thar_order)))
fins_wvs = GLOBALutils.Cheby_eval(coeffs_pix2wav,fins_lns,float(len(thar_order)))
fwhms_wvs = inis_wvs - fins_wvs
resolution2 = wavelengths / fwhms_wvs
if wavelengths.max() > 5500 and wavelengths.min()<5500:
print "\t\t\tmedian Resolution of order", order, '=', np.around(np.median(resolution2))
if (order == 32):
if (use_cheby):
t_ords, t_wavs = [], []
for order in range(nord_ob):
order_s = str(order)
if (order < 10):
order_s = '0' + str(order)
thar_order_orig = lines_thar_ob[order, :]
IV = iv_thar_ob[order, :]
wei = np.sqrt(IV)
bkg = np.zeros(
len(thar_order_orig)
) # - GLOBALutils.Lines_mBack(thar_order_orig, IV, thres_rel=3)
thar_order = thar_order_orig - bkg
coeffs_pix2wav, coeffs_pix2sigma, pixel_centers, wavelengths, rms_ms, residuals, centroids, sigmas, intensities \
= GLOBALutils.Initial_Wav_Calibration( order_dir+'fideos_'+order_s+'.iwdat', thar_order, order, wei, \
rmsmax=10000, minlines=10,FixEnds=False,Dump_Argon=False,Cheby=True,porder=ncoef_x,rough_shift = offset_ob)
if (order == 25):
Global_ZP = GLOBALutils.Cheby_eval(coeffs_pix2wav, 1023,
len(thar_order))
All_Pixel_Centers = np.append(All_Pixel_Centers, pixel_centers)
All_Wavelengths = np.append(All_Wavelengths, wavelengths)
All_Orders = np.append(All_Orders,
np.zeros(len(pixel_centers)) + order)
All_Centroids = np.append(All_Centroids, centroids)
All_Sigmas = np.append(All_Sigmas, sigmas)
All_Intensities = np.append(All_Intensities, intensities)
t_ords.append(order)
t_wavs.append(
GLOBALutils.Cheby_eval(coeffs_pix2wav, 1023, len(thar_order)))