def xidl_arcspec(xidl_file, slit):
xidl_dict = readsav(xidl_file)
if xidl_dict['archive_arc'].ndim == 2:
nspec = xidl_dict['archive_arc'].shape[0]
npix = xidl_dict['archive_arc'].shape[1]
else:
npix = xidl_dict['archive_arc'].shape[0]
# This is the best one (well-centered)
calib = xidl_dict['calib'][slit]
# Generate the wavelengths
if calib['FUNC'] == b'CHEBY':
wv_air = cheby_val(calib['FFIT'], np.arange(npix),
calib['NRM'], calib['NORD'])
elif calib['FUNC'] == b'POLY':
wv_air = poly_val(calib['FFIT'], np.arange(npix), calib['NRM'])
wv_vac = airtovac(wv_air * units.AA)
if xidl_dict['archive_arc'].ndim == 2:
spec = xidl_dict['archive_arc'][slit]
else:
spec = xidl_dict['archive_arc']
# Flip to blue to red?
if wv_vac[1] < wv_vac[0]:
wv_vac = wv_vac[::-1]
spec = spec[::-1]
# Return
return wv_vac.value, spec
def read_ascii(tbl_file, in_vac=True):
"""
The columns need to be wave, flux
And the data should be monoonically increasing in wavelength
Args:
tbl_file (str):
file of the table
in_vac (bool, optional):
If True, wavelenghts are already in vacuum
Returns:
tuple: np.ndarray, np.ndarray of wavelength, flux
"""
arc_spec = Table.read(tbl_file, format='ascii')
# Wavelengths
wv_vac = arc_spec['wave']
if not in_vac:
wv_vac = airtovac(wv_vac * units.AA)
# Return
return wv_vac.value, arc_spec['flux']
def main(flg):
# Keck LRISb
if flg & (2**0): # B300, all lamps
binspec = 1
slits = [15]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B300', 'lris_blue_300.sav')
outroot = 'keck_lris_blue_300_d680.fits'
build_template(xidl_file, slits, None, binspec, outroot, lowredux=True)
if flg & (2**1): # B400, all lamps I think)
binspec = 2
outroot='keck_lris_blue_400_d560.fits'
slits = [19,14]
lcut = [5500.]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B400', 'lris_blue_400_d560.sav')
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
if flg & (2**2): # B600, all lamps
binspec = 2
outroot='keck_lris_blue_600_d560.fits'
slits = [0,7]
lcut = [4500.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'B600', 'MasterWaveCalib_A_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**3): # B1200, all lamps?
binspec = 2
outroot='keck_lris_blue_1200_d460.fits'
slits = [19,44]
lcut = [3700.]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B1200', 'lris_blue_1200.sav')
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
# Shane Kastb
if flg & (2**4): # 452/3306
binspec = 1
slits = [0]
xidl_file = os.path.join(template_path, 'Shane_Kast', '452_3306', 'kast_452_3306.sav')
outroot = 'shane_kast_blue_452.fits'
build_template(xidl_file, slits, None, binspec, outroot, lowredux=True)
if flg & (2**5): # 600/4310
binspec = 1
slits = [0,3]
lcut = [4550.]
xidl_file = os.path.join(template_path, 'Shane_Kast', '600_4310', 'kast_600_4310.sav')
outroot = 'shane_kast_blue_600.fits'
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
if flg & (2**6): # 830/3460
binspec = 1
slits = [0]
xidl_file = os.path.join(template_path, 'Shane_Kast', '830_3460', 'kast_830_3460.sav')
outroot = 'shane_kast_blue_830.fits'
build_template(xidl_file, slits, None, binspec, outroot, lowredux=True)
# Keck/DEIMOS
if flg & (2**7): # 600ZD :: Might not go red enough
binspec = 1
slits = [0,1]
lcut = [7192.]
xidl_file = os.path.join(template_path, 'Keck_DEIMOS', '600ZD', 'deimos_600.sav')
outroot = 'keck_deimos_600.fits'
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
if flg & (2**8): # 830G
binspec = 1
outroot='keck_deimos_830G.fits'
# 3-12 = blue 6508 -- 8410
# 7-24 = blue 8497 -- 9925 (no lines after XeI)
ifiles = [0, 0, 1]
slits = [12, 14, 24]
lcut = [8400., 8480]
wfile1 = os.path.join(template_path, 'Keck_DEIMOS', '830G_M_8600', 'MasterWaveCalib_A_1_03.json')
wfile2 = os.path.join(template_path, 'Keck_DEIMOS', '830G_M_8600', 'MasterWaveCalib_A_1_07.json')
# det_dict
det_cut = {}
det_cut['dets'] = [[1,2,3,4], [5,6,7,8]]
det_cut['wcuts'] = [[0,9000.], [8200,1e9]] # Significant overlap is fine
#
build_template([wfile1,wfile2], slits, lcut, binspec, outroot, lowredux=False,
ifiles=ifiles, det_cut=det_cut)
if flg & (2**9): # 1200
binspec = 1
outroot='keck_deimos_1200G.fits'
# 3-3 = blue 6268.23 -- 7540
# 3-14 = red 6508 -- 7730
# 7-3 = blue 7589 -- 8821
# 7-17 = red 8000 - 9230
# 7c-0 = red 9120 -- 9950
ifiles = [0, 0, 1, 1, 2]
slits = [3, 14, 3, 17, 0]
lcut = [7450., 7730., 8170, 9120]
wfile1 = os.path.join(template_path, 'Keck_DEIMOS', '1200G', 'MasterWaveCalib_A_1_03.json')
wfile2 = os.path.join(template_path, 'Keck_DEIMOS', '1200G', 'MasterWaveCalib_A_1_07.json')
wfile3 = os.path.join(template_path, 'Keck_DEIMOS', '1200G', 'MasterWaveCalib_A_1_07c.json')
# det_dict
det_cut = None
#det_cut = {}
#det_cut['dets'] = [[1,2,3,4], [5,6,7,8]]
#det_cut['wcuts'] = [[0,9000.], [8200,1e9]] # Significant overlap is fine
#
build_template([wfile1,wfile2,wfile3], slits, lcut, binspec, outroot, lowredux=False,
ifiles=ifiles, det_cut=det_cut, chk=True)
# ###############################################3
# Keck/LRISr
if flg & (2**10): # R400
binspec = 2
outroot='keck_lris_red_400.fits'
slits = [7] # Quite blue, but not the bluest
lcut = []
wfile = os.path.join(template_path, 'Keck_LRIS', 'R400', 'MasterWaveCalib_A_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**11): # R1200
# slits = [2-3] # 7726 -- 9250
# slits = [1-4] # 9250 -- 9925
binspec = 1
outroot='keck_lris_red_1200_9000.fits'
ifiles = [0, 1]
slits = [3, 7]
lcut = [9250.]
wfile1 = os.path.join(template_path, 'Keck_LRIS', 'R1200_9000', 'MasterWaveCalib_A_1_02.json') # Original Dev
wfile2 = os.path.join(template_path, 'Keck_LRIS', 'R1200_9000', 'MasterWaveCalib_A_1_01.json') # Dev suite 2x1
build_template([wfile1,wfile2], slits, lcut, binspec, outroot, lowredux=False,
ifiles=ifiles)
if flg & (2**12): # R600/5000
# slits = [1-4] # 5080 -- 7820
# slits = [1-7] # 7820 -- 9170
binspec = 2
outroot='keck_lris_red_600_5000.fits'
slits = [4, 7]
lcut = [7820.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'R600_5000', 'MasterWaveCalib_B_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**27): # R600/7500
# slits = [1-10] # 5000 -- 7840
# slits = [1-4] # 7840 -- 9230
binspec = 2
outroot='keck_lris_red_600_7500.fits'
slits = [10, 4]
lcut = [7840.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'R600_7500', 'MasterWaveCalib_I_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False,
chk=True, normalize=True, subtract_conti=True)
# ##################################
# Magellan/MagE
if flg & (2**13):
# Load
mase_path = os.path.join(os.getenv('XIDL_DIR'), 'Magellan', 'MAGE', 'mase', 'Calib')
sav_file = os.path.join(mase_path, 'MagE_wvguess_jfh.idl')
mase_dict = readsav(sav_file)
mase_sol = Table(mase_dict['all_arcfit'])
# Do it
all_wave = np.zeros((2048, 15))
all_flux = np.zeros_like(all_wave)
for order in np.arange(15):
all_flux[:,order] = mase_dict['sv_aspec'][order]
# Build the wavelengths
wv_air = cheby_val(mase_sol['FFIT'][order], np.arange(2048), mase_sol['NRM'][order],
mase_sol['NORD'][order])
all_wave[:,order] = airtovac(wv_air * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = np.arange(20, 5, -1, dtype=int)
tbl.meta['BINSPEC'] = 1
# Write
outroot='magellan_mage.fits'
outfile = os.path.join(template_path, outroot)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**14): # Magellan/MagE Plots
outpath = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'plots')
new_mage_file = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv',
'magellan_mage.fits')
# Load
mage_wave = Table.read(new_mage_file)
llist = waveio.load_line_lists(['ThAr_MagE'])
#
for kk in range(mage_wave['wave'].shape[1]):
wv = mage_wave['wave'][:, kk]
fx = mage_wave['flux'][:, kk]
order = 20 - kk
# Reidentify
detections, spec_cont_sub, patt_dict = autoid.reidentify(fx, fx, wv, llist, 1)
# Fit
final_fit = fitting.fit_slit(fx, patt_dict, detections, llist)
# Output
outfile=os.path.join(outpath, 'MagE_order{:2d}_IDs.pdf'.format(order))
autoid.arc_fit_qa(final_fit, outfile=outfile, ids_only=True)
print("Wrote: {}".format(outfile))
autoid.arc_fit_qa(final_fit, outfile=os.path.join(outpath, 'MagE_order{:2d}_full.pdf'.format(order)))
if flg & (2**15): # VLT/X-Shooter reid_arxiv
# VIS
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
for iroot, iout in zip(['vlt_xshooter_vis1x1.json', 'vlt_xshooter_nir.json'],
['vlt_xshooter_vis1x1.fits', 'vlt_xshooter_nir.fits']):
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk,order in enumerate(orders):
all_flux[:,kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:,kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:,kk] = airtovac(odict[str(kk)]['wave_soln'] * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**16): # VLT/X-Shooter line list
line_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'lists')
old_file = os.path.join(line_path, 'ThAr_XSHOOTER_VIS_air_lines.dat')
# Load
air_list = waveio.load_line_list(old_file)
# Vacuum
vac_wv = airtovac(air_list['wave']*units.AA).value
vac_list = air_list.copy()
vac_list['wave'] = vac_wv
# Write
new_file = os.path.join(line_path, 'ThAr_XSHOOTER_VIS_lines.dat')
vac_list.write(new_file, format='ascii.fixed_width', overwrite=True)
print("Wrote: {}".format(new_file))
if flg & (2**17): # NIRES
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
iroot = 'keck_nires.json'
iout = 'keck_nires.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk,order in enumerate(orders):
all_flux[:,kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:,kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:,kk] = airtovac(odict[str(kk)]['wave_soln'] * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**18): # Gemini/GNIRS
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
iroot = 'gemini_gnirs.json'
iout = 'gemini_gnirs.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk,order in enumerate(orders):
all_flux[:,kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:,kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:,kk] = airtovac(odict[str(kk)]['wave_soln'] * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
# ##############################
if flg & (2**20): # GMOS R400 Hamamatsu
binspec = 2
outroot='gemini_gmos_r400_ham.fits'
#
ifiles = [0, 1, 2, 3, 4]
slits = [0, 2, 3, 0, 0] # Be careful with the order..
lcut = [5400., 6620., 8100., 9000.]
wfile1 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_01_aa.json')
wfile5 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_05_aa.json') # 5190 -- 6679
#wfile2 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_02_aa.json')
wfile3 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_04_aa.json')
wfile4 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_03_aa.json')
wfile6 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_06_aa.json')
#
build_template([wfile1,wfile5,wfile3,wfile4, wfile6], slits, lcut, binspec,
outroot, lowredux=False, ifiles=ifiles, chk=True,
normalize=True, subtract_conti=True)
# ##############################
if flg & (2**21): # GMOS R400 E2V
binspec = 2
outroot='gemini_gmos_r400_e2v.fits'
#
ifiles = [0, 1, 2]
slits = [0, 0, 0]
lcut = [6000., 7450]
wfile1 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_1_01.json')
wfile2 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_1_02.json')
wfile3 = os.path.join(template_path, 'GMOS', 'R400', 'MasterWaveCalib_A_1_03.json')
#
build_template([wfile1,wfile2,wfile3], slits, lcut, binspec,
outroot, lowredux=False, ifiles=ifiles, chk=True,
normalize=True)
# ##############################
if flg & (2**22): # GMOS R400 Hamamatsu
binspec = 2
outroot='gemini_gmos_b600_ham.fits'
#
ifiles = [0, 1, 2, 3, 4]
slits = [0, 0, 0, 0, 0]
lcut = [4250., 4547., 5250., 5615.]
wfile1 = os.path.join(template_path, 'GMOS', 'B600', 'MasterWaveCalib_C_1_01.json')
wfile5 = os.path.join(template_path, 'GMOS', 'B600', 'MasterWaveCalib_D_1_01.json') # - 4547
wfile2 = os.path.join(template_path, 'GMOS', 'B600', 'MasterWaveCalib_C_1_02.json')
wfile4 = os.path.join(template_path, 'GMOS', 'B600', 'MasterWaveCalib_D_1_02.json') # 4610-5608
wfile3 = os.path.join(template_path, 'GMOS', 'B600', 'MasterWaveCalib_C_1_03.json')
#
build_template([wfile1,wfile5,wfile2,wfile4,wfile3], slits, lcut, binspec,
outroot, lowredux=False, ifiles=ifiles, chk=True,
normalize=True, subtract_conti=True, miny=-100.)
if flg & (2**23): # WHT/ISIS
iroot = 'wht_isis_blue_1200_4800.json'
outroot = 'wht_isis_blue_1200_4800.fits'
wfile = os.path.join(template_path, 'WHT_ISIS', '1200B', iroot)
binspec = 2
slits = [0]
lcut = [3200.]
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**24): # Magellan/FIRE
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
iroot = 'magellan_fire_echelle.json'
iout = 'magellan_fire_echelle.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk,order in enumerate(orders):
all_flux[:,kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:,kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:,kk] = airtovac(odict[str(kk)]['wave_soln'] * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**25): # FIRE longslit
binspec = 1
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
outroot = 'magellan_fire_long.fits'
xidl_file = os.path.join(os.getenv('FIRE_DIR'), 'LowDispersion', 'NeNeAr_archive_fit.fits')
spec_file = os.path.join(os.getenv('FIRE_DIR'), 'LowDispersion', 'NeNeAr2.sav')
fire_sol = Table.read(xidl_file)
wave = cheby_val(fire_sol['FFIT'].data[0], np.arange(2048), fire_sol['NRM'].data[0], fire_sol['NORD'].data[0])
wv_vac = airtovac(wave * units.AA)
xidl_dict = readsav(spec_file)
flux = xidl_dict['arc1d']
write_template(wv_vac.value, flux, binspec, reid_path, outroot, det_cut=None)
# Gemini/Flamingos2
if flg & (2**26):
reid_path = os.path.join(resource_filename('pypeit', 'data'), 'arc_lines', 'reid_arxiv')
iroot = ['Flamingos2_JH_JH.json','Flamingos2_HK_HK.json']
outroot=['Flamingos2_JH_JH.fits','Flamingos2_HK_HK.fits']
binspec = 1
slits = [0]
lcut = []
for ii in range(len(iroot)):
wfile = os.path.join(reid_path, iroot[ii])
build_template(wfile, slits, lcut, binspec, outroot[ii], lowredux=False)
# MDM/OSMOS -- MDM4K
if flg & (2 ** 28):
# ArI 4159 -- 6800
wfile = os.path.join(template_path, 'MDM_OSMOS', 'MasterWaveCalib_MDM4K_01.json')
outroot = 'mdm_osmos_mdm4k.fits'
binspec = 1
slits = [0]
lcut = [3200.]
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False,
chk=True, subtract_conti=True)
def create_linelist(wavelength,
spec,
fwhm,
sigdetec=2.,
cont_samp=10.,
line_name=None,
file_root_name=None,
iraf_frmt=False,
debug=False,
convert_air_to_vac=True):
""" Create list of lines detected in a spectrum in a PypeIt
compatible format. The name of the output file is
file_root_name+'_lines.dat'.
Parameters
----------
wavelength : np.array
wavelength
spec : np.array
spectrum
fwhm : float
fwhm in pixels used for filtering out arc lines that are too
wide and not considered in fits. Parameter of arc.detect_lines().
sigdetec : float
sigma threshold above fluctuations for line detection. Parameter
of arc.detect_lines(). Default = 2.
cont_samp : float
the number of samples across the spectrum used for continuum
subtraction. Parameter of arc.detect_lines(). Default = 10.
line_name : str
name of the lines to listed in the file.
file_root_name : str
name of the file where the identified lines will be stored.
The code automatically add '_lines.dat' at the end of the
root name.
iraf_frmt : bool
if True, the file is written in the IRAF format (i.e. wavelength,
ion name, amplitude).
convert_air_to_vac (bool):
If True, convert the wavelengths of the created linelist from air to vacuum
"""
msgs.info("Searching for peaks {} sigma above background".format(sigdetec))
tampl_true, tampl, tcent, twid, centerr, ww, arcnorm, nsig = arc.detect_lines(
spec, sigdetect=sigdetec, fwhm=fwhm, cont_samp=cont_samp, debug=debug)
peaks_good = tcent[ww]
ampl_good = tampl[ww]
# convert from pixel location to wavelength
pixvec = np.arange(spec.size)
wave_peak = scipy.interpolate.interp1d(
pixvec, wavelength, bounds_error=False,
fill_value='extrapolate')(peaks_good)
# Convert to vacuum?
if convert_air_to_vac:
msgs.info("Converting wavelengths from air to vacuum")
wave_peak = airtovac(wave_peak * units.AA).value
npeak = len(wave_peak)
ion = npeak * [str(line_name)]
NIST = npeak * [1]
Instr = npeak * [32]
Source = npeak * ['wavemodel.py']
if iraf_frmt:
msgs.info("Printing file in IRAF format: {}".format(file_root_name +
'_iraf_lines.dat'))
ion = np.array(ion)
id_lines_iraf = np.vstack((np.round(wave_peak,
5), ion, np.round(ampl_good, 5))).T
np.savetxt(file_root_name + '_iraf_lines.dat',
id_lines_iraf,
fmt="%15s %6s %15s",
delimiter=" ")
else:
msgs.info("Printing file: {}".format(file_root_name + '_lines.dat'))
dat = Table([wave_peak, ion, NIST, Instr, ampl_good, Source],
names=('wave', 'ion', 'NIST', 'Instr', 'amplitude',
'Source'))
dat.write(file_root_name + '_lines.dat', format='ascii.fixed_width')
def main(flg):
# Keck LRISb
if flg & (2**0): # B300, all lamps
binspec = 1
slits = [15]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B300',
'lris_blue_300.sav')
outroot = 'keck_lris_blue_300_d680.fits'
build_template(xidl_file, slits, None, binspec, outroot, lowredux=True)
if flg & (2**1): # B400, all lamps I think)
binspec = 2
outroot = 'keck_lris_blue_400_d560.fits'
slits = [19, 14]
lcut = [5500.]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B400',
'lris_blue_400_d560.sav')
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
if flg & (2**2): # B600, all lamps
binspec = 2
outroot = 'keck_lris_blue_600_d560.fits'
slits = [0, 7]
lcut = [4500.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'B600',
'MasterWaveCalib_A_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**3): # B1200, all lamps?
binspec = 2
outroot = 'keck_lris_blue_1200_d460.fits'
slits = [19, 44]
lcut = [3700.]
xidl_file = os.path.join(template_path, 'Keck_LRIS', 'B1200',
'lris_blue_1200.sav')
build_template(xidl_file, slits, lcut, binspec, outroot, lowredux=True)
# ###############################################3
# Keck/LRISr
if flg & (2**10): # R400
binspec = 2
outroot = 'keck_lris_red_400.fits'
slits = [7] # Quite blue, but not the bluest
lcut = []
wfile = os.path.join(template_path, 'Keck_LRIS', 'R400',
'MasterWaveCalib_A_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**11): # R1200
# slits = [2-3] # 7726 -- 9250
# slits = [1-4] # 9250 -- 9925
binspec = 1
outroot = 'keck_lris_red_1200_9000.fits'
ifiles = [0, 1]
slits = [3, 7]
lcut = [9250.]
wfile1 = os.path.join(template_path, 'Keck_LRIS', 'R1200_9000',
'MasterWaveCalib_A_1_02.json') # Original Dev
wfile2 = os.path.join(template_path, 'Keck_LRIS', 'R1200_9000',
'MasterWaveCalib_A_1_01.json') # Dev suite 2x1
build_template([wfile1, wfile2],
slits,
lcut,
binspec,
outroot,
lowredux=False,
ifiles=ifiles)
if flg & (2**12): # R600/5000
# slits = [1-4] # 5080 -- 7820
# slits = [1-7] # 7820 -- 9170
binspec = 2
outroot = 'keck_lris_red_600_5000.fits'
slits = [4, 7]
lcut = [7820.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'R600_5000',
'MasterWaveCalib_B_1_01.json')
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**27): # R600/7500
# slits = [1-10] # 5000 -- 7840
# slits = [1-4] # 7840 -- 9230
binspec = 2
outroot = 'keck_lris_red_600_7500.fits'
slits = [10, 4]
lcut = [7840.]
wfile = os.path.join(template_path, 'Keck_LRIS', 'R600_7500',
'MasterWaveCalib_I_1_01.json')
build_template(wfile,
slits,
lcut,
binspec,
outroot,
lowredux=False,
chk=True,
normalize=True,
subtract_conti=True)
# ##################################
# Magellan/MagE
if flg & (2**13):
# Load
mase_path = os.path.join(os.getenv('XIDL_DIR'), 'Magellan', 'MAGE',
'mase', 'Calib')
sav_file = os.path.join(mase_path, 'MagE_wvguess_jfh.idl')
mase_dict = readsav(sav_file)
mase_sol = Table(mase_dict['all_arcfit'])
# Do it
all_wave = np.zeros((2048, 15))
all_flux = np.zeros_like(all_wave)
for order in np.arange(15):
all_flux[:, order] = mase_dict['sv_aspec'][order]
# Build the wavelengths
wv_air = cheby_val(mase_sol['FFIT'][order], np.arange(2048),
mase_sol['NRM'][order], mase_sol['NORD'][order])
all_wave[:, order] = airtovac(wv_air * units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = np.arange(20, 5, -1, dtype=int)
tbl.meta['BINSPEC'] = 1
# Write
outroot = 'magellan_mage.fits'
outfile = os.path.join(template_path, outroot)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**14): # Magellan/MagE Plots
outpath = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'plots')
new_mage_file = os.path.join(resource_filename('pypeit',
'data'), 'arc_lines',
'reid_arxiv', 'magellan_mage.fits')
# Load
mage_wave = Table.read(new_mage_file)
llist = waveio.load_line_lists(['ThAr_MagE'])
#
for kk in range(mage_wave['wave'].shape[1]):
wv = mage_wave['wave'][:, kk]
fx = mage_wave['flux'][:, kk]
order = 20 - kk
# Reidentify
detections, spec_cont_sub, patt_dict = autoid.reidentify(
fx, fx, wv, llist, 1)
# Fit
final_fit = wv_fitting.fit_slit(fx, patt_dict, detections, llist)
# Output
outfile = os.path.join(outpath,
'MagE_order{:2d}_IDs.pdf'.format(order))
autoid.arc_fit_qa(final_fit, outfile=outfile, ids_only=True)
print("Wrote: {}".format(outfile))
autoid.arc_fit_qa(final_fit,
outfile=os.path.join(
outpath,
'MagE_order{:2d}_full.pdf'.format(order)))
if flg & (2**15): # VLT/X-Shooter reid_arxiv
# VIS
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
for iroot, iout in zip(
['vlt_xshooter_vis1x1.json', 'vlt_xshooter_nir.json'],
['vlt_xshooter_vis1x1.fits', 'vlt_xshooter_nir.fits']):
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk, order in enumerate(orders):
all_flux[:, kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:, kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:, kk] = airtovac(odict[str(kk)]['wave_soln'] *
units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**16): # VLT/X-Shooter line list
line_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'lists')
old_file = os.path.join(line_path, 'ThAr_XSHOOTER_VIS_air_lines.dat')
# Load
air_list = waveio.load_line_list(old_file)
# Vacuum
vac_wv = airtovac(air_list['wave'] * units.AA).value
vac_list = air_list.copy()
vac_list['wave'] = vac_wv
# Write
new_file = os.path.join(line_path, 'ThAr_XSHOOTER_VIS_lines.dat')
vac_list.write(new_file, format='ascii.fixed_width', overwrite=True)
print("Wrote: {}".format(new_file))
if flg & (2**17): # NIRES
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = 'keck_nires.json'
iout = 'keck_nires.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk, order in enumerate(orders):
all_flux[:, kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:, kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:, kk] = airtovac(odict[str(kk)]['wave_soln'] *
units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**18): # Gemini/GNIRS
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = 'gemini_gnirs.json'
iout = 'gemini_gnirs.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk, order in enumerate(orders):
all_flux[:, kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:, kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:, kk] = airtovac(odict[str(kk)]['wave_soln'] *
units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**23): # WHT/ISIS
iroot = 'wht_isis_blue_1200_4800.json'
outroot = 'wht_isis_blue_1200_4800.fits'
wfile = os.path.join(template_path, 'WHT_ISIS', '1200B', iroot)
binspec = 2
slits = [0]
lcut = [3200.]
build_template(wfile, slits, lcut, binspec, outroot, lowredux=False)
if flg & (2**24): # Magellan/FIRE
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = 'magellan_fire_echelle.json'
iout = 'magellan_fire_echelle.fits'
# Load
old_file = os.path.join(reid_path, iroot)
odict, par = waveio.load_reid_arxiv(old_file)
# Do it
orders = odict['fit2d']['orders'][::-1].astype(int) # Flipped
all_wave = np.zeros((odict['0']['nspec'], orders.size))
all_flux = np.zeros_like(all_wave)
for kk, order in enumerate(orders):
all_flux[:, kk] = odict[str(kk)]['spec']
if 'nir' in iroot:
all_wave[:, kk] = odict[str(kk)]['wave_soln']
else:
all_wave[:, kk] = airtovac(odict[str(kk)]['wave_soln'] *
units.AA).value
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
if flg & (2**25): # FIRE longslit
binspec = 1
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
outroot = 'magellan_fire_long.fits'
xidl_file = os.path.join(os.getenv('FIRE_DIR'), 'LowDispersion',
'NeNeAr_archive_fit.fits')
spec_file = os.path.join(os.getenv('FIRE_DIR'), 'LowDispersion',
'NeNeAr2.sav')
fire_sol = Table.read(xidl_file)
wave = cheby_val(fire_sol['FFIT'].data[0], np.arange(2048),
fire_sol['NRM'].data[0], fire_sol['NORD'].data[0])
wv_vac = airtovac(wave * units.AA)
xidl_dict = readsav(spec_file)
flux = xidl_dict['arc1d']
wvutils.write_template(wv_vac.value,
flux,
binspec,
reid_path,
outroot,
det_cut=None)
# Gemini/Flamingos2
if flg & (2**26):
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = ['Flamingos2_JH_JH.json', 'Flamingos2_HK_HK.json']
outroot = ['Flamingos2_JH_JH.fits', 'Flamingos2_HK_HK.fits']
binspec = 1
slits = [0]
lcut = []
for ii in range(len(iroot)):
wfile = os.path.join(reid_path, iroot[ii])
build_template(wfile,
slits,
lcut,
binspec,
outroot[ii],
lowredux=False)
# MDM/OSMOS -- MDM4K
if flg & (2**28):
# ArI 4159 -- 6800
wfile = os.path.join(template_path, 'MDM_OSMOS',
'MasterWaveCalib_MDM4K_01.json')
outroot = 'mdm_osmos_mdm4k.fits'
binspec = 1
slits = [0]
lcut = [3200.]
build_template(wfile,
slits,
lcut,
binspec,
outroot,
lowredux=False,
chk=True,
subtract_conti=True)
# Keck KCWI
if flg & (2**29):
# FeAr BH2
wfile1 = os.path.join(template_path, 'KCWI', 'BH2',
'Keck_KCWI_BH2_4200.json')
outroot = 'keck_kcwi_BH2_4200.fits'
binspec = 1
slits = [1015]
lcut = [4350.0, 8000.0]
build_template([wfile1],
slits,
lcut,
binspec,
outroot,
lowredux=False,
normalize=True)
# FeAr BM
wfile1 = os.path.join(template_path, 'KCWI', 'BM',
'Keck_KCWI_BM_4060.json')
wfile2 = os.path.join(template_path, 'KCWI', 'BM',
'Keck_KCWI_BM_4670.json')
outroot = 'keck_kcwi_BM.fits'
binspec = 1
slits = [1026, 1021]
lcut = [4350.0, 8000.0]
build_template([wfile1, wfile2],
slits,
lcut,
binspec,
outroot,
lowredux=False,
normalize=True)
# P200 DBSP r
if flg & (2**30):
# HeNeAr
wfile = os.path.join(template_path, 'P200_DBSP', 'R316_7500_D55',
'P200_DBSP_Red.json')
outroot = 'p200_dbsp_red_316_7500_d55.fits'
binspec = 1
slits = [221]
lcut = None # only matters if >1 slit
build_template([wfile],
slits,
lcut,
binspec,
outroot,
lowredux=False,
normalize=True)
# P200 DBSP b
if flg & (2**31):
# FeAr
wfile = os.path.join(template_path, 'P200_DBSP', 'B600_4000_D55',
'P200_DBSP_Blue.json')
outroot = 'p200_dbsp_blue_600_4000_d55.fits'
binspec = 1
slits = [231]
lcut = None
build_template([wfile],
slits,
lcut,
binspec,
outroot,
lowredux=False,
normalize=True)
# MMT/MMIRS
if flg & (2**32):
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = [
'mmt_mmirs_HK_zJ.json', 'mmt_mmirs_J_zJ.json',
'mmt_mmirs_K3000_Kspec.json'
]
outroot = [
'mmt_mmirs_HK_zJ.fits', 'mmt_mmirs_J_zJ.fits',
'mmt_mmirs_K3000_Kspec.fits'
]
binspec = 1
slits = [1020, 1020, 1020]
lcut = []
for ii in range(len(iroot)):
wfile = os.path.join(reid_path, iroot[ii])
build_template(wfile,
slits,
lcut,
binspec,
outroot[ii],
lowredux=False)
# LBT/MODS
if flg & (2**33):
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = ['lbt_mods1r_red.json', 'lbt_mods2r_red.json']
outroot = ['lbt_mods1r_red.fits', 'lbt_mods2r_red.fits']
binspec = 1
slits = [[1557], [1573]]
lcut = []
for ii in range(len(iroot)):
wfile = os.path.join(reid_path, iroot[ii])
build_template(wfile,
slits[ii],
lcut,
binspec,
outroot[ii],
lowredux=False)
# P200 Triplespec
if flg & (2**34):
reid_path = os.path.join(resource_filename('pypeit', 'data'),
'arc_lines', 'reid_arxiv')
iroot = 'p200_triplespec_MasterWaveCalib.fits'
iout = 'p200_triplespec.fits'
# Load
old_file = os.path.join(reid_path, iroot)
par = io.fits_open(old_file)
pyp_spec = par[0].header['PYP_SPEC']
spectrograph = load_spectrograph(pyp_spec)
orders = spectrograph.orders
# Do it
all_wave = np.zeros((par[2].data['spec'].size, orders.size))
all_flux = np.zeros_like(all_wave)
for kk, order in enumerate(orders):
all_flux[:, kk] = par[2 * kk + 2].data['spec']
all_wave[:, kk] = par[2 * kk + 2].data['wave_soln']
# Write
tbl = Table()
tbl['wave'] = all_wave.T
tbl['flux'] = all_flux.T
tbl['order'] = orders
tbl.meta['BINSPEC'] = 1
# Write
outfile = os.path.join(reid_path, iout)
tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
