bypass=bypassflag)
Wavelength.fit_lambda(maskname, band, argon, argon, waveops, longslit=longslit)
Wavelength.apply_lambda_simple(maskname,
band,
argon,
waveops,
longslit=longslit,
smooth=True)
# make sure you use the correct wavelength file generated before
Wavelength_file = 'lambda_solution_wave_stack_H_m150428_0091-0091.fits'
# narrow
Background.handle_background(obsfiles_posAnarrow,
Wavelength_file,
maskname,
band,
waveops,
target=target_posAnarrow)
Background.handle_background(obsfiles_posCnarrow,
Wavelength_file,
maskname,
band,
waveops,
target=target_posCnarrow)
# wide
Background.handle_background(obsfiles_posAwide,
Wavelength_file,
maskname,
band,
waveops,
target=target_posAwide)
def handle_rectification(maskname, in_files, wavename, band_pass, barset_file, options,
commissioning_shift=3.0):
'''Handle slit rectification and coaddition.
Args:
maskname: The mask name string
in_files: List of stacked spectra in electron per second. Will look
like ['electrons_Offset_1.5.txt.fits', 'electrons_Offset_-1.5.txt.fits']
wavename: path (relative or full) to the wavelength stack file, string
band_pass: Band pass name, string
barset_file: Path to a mosfire fits file containing the full set of
FITS extensions for the barset. It can be any file in the list
of science files.
Returns:
None
Writes files:
[maskname]_[band]_[object name]_eps.fits --
The rectified, background subtracted, stacked eps spectrum
[maskname]_[band]_[object name]_sig.fits --
Rectified, background subtracted, stacked weight spectrum (STD/itime)
[maskname]_[band]_[object_name]_itime.fits
Rectified, CRR stacked integration time spectrum
[maskname]_[band]_[object_name]_snrs.fits
Rectified signal to noise spectrum
'''
global edges, dats, vars, itimes, shifts, lambdas, band, fidl, all_shifts
band = band_pass
dlambda = Wavelength.grating_results(band)
hpp = Filters.hpp[band]
fidl = np.arange(hpp[0], hpp[1], dlambda)
lambdas = IO.readfits(wavename, options)
if np.any(lambdas[1].data < 0) or np.any(lambdas[1].data > 29000):
print "***********WARNING ***********"
print "The file {0} may not be a wavelength file.".format(wavename)
print "Check before proceeding."
print "***********WARNING ***********"
edges, meta = IO.load_edges(maskname, band, options)
shifts = []
posnames = []
postoshift = {}
for file in in_files:
print ":: ", file
II = IO.read_drpfits(maskname, file, options)
off = np.array((II[0]["decoff"], II[0]["raoff"]),dtype=np.float64)
if "yoffset" in II[0]:
off = -II[0]["yoffset"]
else:
# Deal with data taken during commissioning
if II[0]["frameid"] == 'A': off = 0.0
else: off = commissioning_shift
try: off0
except: off0 = off
shift = off - off0
shifts.append(shift)
posnames.append(II[0]["frameid"])
postoshift[II[0]['frameid']] = shift
print "Position {0} shift: {1:2.2f} as".format(off, shift)
plans = Background.guess_plan_from_positions(set(posnames))
all_shifts = []
for plan in plans:
to_append = []
for pos in plan:
to_append.append(postoshift[pos])
all_shifts.append(to_append)
# Reverse the elements in all_shifts to deal with an inversion
all_shifts.reverse()
theBPM = IO.badpixelmask()
all_solutions = []
cntr = 0
for plan in plans:
p0 = plan[0].replace("'", "p")
p1 = plan[1].replace("'", "p")
suffix = "%s-%s" % (p0,p1)
print "Handling plan %s" % suffix
fname = "bsub_{0}_{1}_{2}.fits".format(maskname,band,suffix)
EPS = IO.read_drpfits(maskname, fname, options)
EPS[1] = np.ma.masked_array(EPS[1], theBPM, fill_value=0)
fname = "var_{0}_{1}_{2}.fits".format(maskname, band, suffix)
VAR = IO.read_drpfits(maskname, fname, options)
VAR[1] = np.ma.masked_array(VAR[1], theBPM, fill_value=np.inf)
fname = "itime_{0}_{1}_{2}.fits".format(maskname, band, suffix)
ITIME = IO.read_drpfits(maskname, fname, options)
ITIME[1] = np.ma.masked_array(ITIME[1], theBPM, fill_value=0)
dats = EPS
vars = VAR
itimes = ITIME
EPS[0]["ORIGFILE"] = fname
tock = time.time()
sols = range(len(edges)-1,-1,-1)
shifts = all_shifts[cntr]
cntr += 1
p = Pool()
solutions = p.map(handle_rectification_helper, sols)
#solutions = map(handle_rectification_helper, [15])
p.close()
all_solutions.append(solutions)
tick = time.time()
print "-----> Mask took %i. Writing to disk." % (tick-tock)
output = np.zeros((1, len(fidl)))
snrs = np.zeros((1, len(fidl)))
sdout= np.zeros((1, len(fidl)))
itout= np.zeros((1, len(fidl)))
# the barset [bs] is used for determining object position
x, x, bs = IO.readmosfits(barset_file, options)
for i_slit in xrange(len(solutions)):
solution = all_solutions[0][i_slit]
header = EPS[0].copy()
obj = header['OBJECT']
target_name = bs.ssl[-(i_slit+1)]['Target_Name']
header['OBJECT'] = target_name
pixel_dist = np.float(bs.ssl[-(i_slit+1)]['Target_to_center_of_slit_distance'])/0.18
pixel_dist -= solution['offset']
ll = solution["lambda"]
header["wat0_001"] = "system=world"
header["wat1_001"] = "wtype=linear"
header["wat2_001"] = "wtype=linear"
header["dispaxis"] = 1
header["dclog1"] = "Transform"
header["dc-flag"] = 0
header["ctype1"] = "AWAV"
header["cunit1"] = "Angstrom"
header["crval1"] = ll[0]
header["crval2"] = -solution["eps_img"].shape[0]/2 - pixel_dist
header["crpix1"] = 1
header["crpix2"] = 1
header["cdelt1"] = 1
header["cdelt2"] = 1
header["cname1"] = "angstrom"
header["cname2"] = "pixel"
header["cd1_1"] = ll[1]-ll[0]
header["cd1_2"] = 0
header["cd2_1"] = 0
header["cd2_2"] = 1
S = output.shape
img = solution["eps_img"]
std = solution["sd_img"]
tms = solution["itime_img"]
for i_solution in xrange(1,len(all_solutions)):
print "Combining solution %i" %i_solution
solution = all_solutions[i_solution][i_slit]
img += solution["eps_img"]
std += solution["sd_img"]
tms += solution["itime_img"]
output = np.append(output, img, 0)
output = np.append(output, np.nan*np.zeros((3,S[1])), 0)
snrs = np.append(snrs, img*tms/std, 0)
snrs = np.append(snrs, np.nan*np.zeros((3,S[1])), 0)
sdout = np.append(sdout, std, 0)
sdout = np.append(sdout, np.nan*np.zeros((3,S[1])), 0)
itout = np.append(itout, tms, 0)
itout = np.append(itout, np.nan*np.zeros((3,S[1])), 0)
header['bunit'] = ('electron/second', 'electron power')
IO.writefits(img, maskname,
"{0}_{1}_{2}_eps.fits".format(maskname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('electron/second', 'sigma/itime')
IO.writefits(std/tms, maskname,
"{0}_{1}_{2}_sig.fits".format(maskname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('second', 'exposure time')
IO.writefits(tms, maskname,
"{0}_{1}_{2}_itime.fits".format(maskname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('', 'SNR')
IO.writefits(img*tms/std, maskname,
"{0}_{1}_{2}_snrs.fits".format(maskname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header = EPS[0].copy()
header["wat0_001"] = "system=world"
header["wat1_001"] = "wtype=linear"
header["wat2_001"] = "wtype=linear"
header["dispaxis"] = 1
header["dclog1"] = "Transform"
header["dc-flag"] = 0
header["ctype1"] = "AWAV"
header["cunit1"] = ("Angstrom", 'Start wavelength')
header["crval1"] = ll[0]
header["crval2"] = 1
header["crpix1"] = 1
header["crpix2"] = 1
header["cdelt1"] = 1
header["cdelt2"] = 1
header["cname1"] = "angstrom"
header["cname2"] = "pixel"
header["cd1_1"] = (ll[1]-ll[0], 'Angstrom/pixel')
header["cd1_2"] = 0
header["cd2_1"] = 0
header["cd2_2"] = 1
header["bunit"] = "ELECTRONS/SECOND"
IO.writefits(output, maskname, "{0}_{1}_eps.fits".format(maskname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = ""
IO.writefits(snrs, maskname, "{0}_{1}_snrs.fits".format(maskname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = "ELECTRONS/SECOND"
IO.writefits(sdout/itout, maskname, "{0}_{1}_sig.fits".format(maskname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = "SECOND"
IO.writefits(itout, maskname, "{0}_{1}_itime.fits".format(maskname,
band), options, overwrite=True, header=header,
lossy_compress=False)
def handle_rectification(maskname, in_files, wavename, band_pass, files, options,
commissioning_shift=3.0, target='default'):
'''Handle slit rectification and coaddition.
Args:
maskname: The mask name string
in_files: List of stacked spectra in electron per second. Will look
like ['electrons_Offset_1.5.txt.fits', 'electrons_Offset_-1.5.txt.fits']
wavename: path (relative or full) to the wavelength stack file, string
band_pass: Band pass name, string
barset_file: Path to a mosfire fits file containing the full set of
FITS extensions for the barset. It can be any file in the list
of science files.
Returns:
None
Writes files:
[maskname]_[band]_[object name]_eps.fits --
The rectified, background subtracted, stacked eps spectrum
[maskname]_[band]_[object name]_sig.fits --
Rectified, background subtracted, stacked weight spectrum (STD/itime)
[maskname]_[band]_[object_name]_itime.fits
Rectified, CRR stacked integration time spectrum
[maskname]_[band]_[object_name]_snrs.fits
Rectified signal to noise spectrum
'''
global edges, dats, vars, itimes, shifts, lambdas, band, fidl, all_shifts
band = band_pass
dlambda = Wavelength.grating_results(band)
hpp = Filters.hpp[band]
fidl = np.arange(hpp[0], hpp[1], dlambda)
lambdas = IO.readfits(wavename, options)
if np.any(lambdas[1].data < 0) or np.any(lambdas[1].data > 29000):
info("***********WARNING ***********")
info("The file {0} may not be a wavelength file.".format(wavename))
info("Check before proceeding.")
info("***********WARNING ***********")
edges, meta = IO.load_edges(maskname, band, options)
shifts = []
posnames = []
postoshift = {}
for file in in_files:
info(":: "+str(file))
II = IO.read_drpfits(maskname, file, options)
off = np.array((II[0]["decoff"], II[0]["raoff"]),dtype=np.float64)
if "yoffset" in II[0]:
off = -II[0]["yoffset"]
else:
# Deal with data taken during commissioning
if II[0]["frameid"] == 'A': off = 0.0
else: off = commissioning_shift
try: off0
except: off0 = off
shift = off - off0
shifts.append(shift)
posnames.append(II[0]["frameid"])
postoshift[II[0]['frameid']] = shift
info("Position {0} shift: {1:2.2f} as".format(off, shift))
# this is to deal with cases in which we want to rectify one single file
if len(set(posnames)) is 1:
plans = [['A']]
else:
plans = Background.guess_plan_from_positions(set(posnames))
all_shifts = []
for plan in plans:
to_append = []
for pos in plan:
to_append.append(postoshift[pos])
all_shifts.append(to_append)
# Reverse the elements in all_shifts to deal with an inversion
all_shifts.reverse()
theBPM = IO.badpixelmask()
all_solutions = []
cntr = 0
if target is 'default':
outname = maskname
else:
outname = target
for plan in plans:
if len(plan) is 1:
p0 = 'A'
p1 = 'B'
else:
p0 = plan[0].replace("'", "p")
p1 = plan[1].replace("'", "p")
suffix = "%s-%s" % (p0,p1)
info("Handling plan %s" % suffix)
fname = "bsub_{0}_{1}_{2}.fits".format(outname,band,suffix)
EPS = IO.read_drpfits(maskname, fname, options)
EPS[1] = np.ma.masked_array(EPS[1], theBPM, fill_value=0)
fname = "var_{0}_{1}_{2}.fits".format(outname, band, suffix)
VAR = IO.read_drpfits(maskname, fname, options)
VAR[1] = np.ma.masked_array(VAR[1], theBPM, fill_value=np.inf)
fname = "itime_{0}_{1}_{2}.fits".format(outname, band, suffix)
ITIME = IO.read_drpfits(maskname, fname, options)
ITIME[1] = np.ma.masked_array(ITIME[1], theBPM, fill_value=0)
dats = EPS
vars = VAR
itimes = ITIME
EPS[0]["ORIGFILE"] = fname
tock = time.time()
sols = range(len(edges)-1,-1,-1)
shifts = all_shifts[cntr]
cntr += 1
p = Pool()
solutions = p.map(handle_rectification_helper, sols)
p.close()
all_solutions.append(solutions)
tick = time.time()
info("-----> Mask took %i. Writing to disk." % (tick-tock))
output = np.zeros((1, len(fidl)))
snrs = np.zeros((1, len(fidl)))
sdout= np.zeros((1, len(fidl)))
itout= np.zeros((1, len(fidl)))
# the barset [bs] is used for determining object position
files = IO.list_file_to_strings(files)
info("Using "+str(files[0])+" for slit configuration.")
x, x, bs = IO.readmosfits(files[0], options)
for i_slit in xrange(len(solutions)):
solution = all_solutions[0][i_slit]
header = EPS[0].copy()
obj = header['OBJECT']
target_name = bs.ssl[-(i_slit+1)]['Target_Name']
header['OBJECT'] = target_name
pixel_dist = np.float(bs.ssl[-(i_slit+1)]['Target_to_center_of_slit_distance'])/0.18
pixel_dist -= solution['offset']
ll = solution["lambda"]
header["wat0_001"] = "system=world"
header["wat1_001"] = "wtype=linear"
header["wat2_001"] = "wtype=linear"
header["dispaxis"] = 1
header["dclog1"] = "Transform"
header["dc-flag"] = 0
header["ctype1"] = "AWAV"
header["cunit1"] = "Angstrom"
header["crval1"] = ll[0]
header["crval2"] = -solution["eps_img"].shape[0]/2 - pixel_dist
header["crpix1"] = 1
header["crpix2"] = 1
#remove redundant CDELTi due to wavelength issues with ds9
#see: https://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/44
#header["cdelt1"] = 1
#header["cdelt2"] = 1
header["cname1"] = "angstrom"
header["cname2"] = "pixel"
header["cd1_1"] = ll[1]-ll[0]
header["cd1_2"] = 0
header["cd2_1"] = 0
header["cd2_2"] = 1
try:
header["BARYCORR"]= (lambdas[0]['BARYCORR'],lambdas[0].comments['BARYCORR'])
except KeyError:
warning( "Barycentric corrections not applied to the wavelength solution")
pass
S = output.shape
img = solution["eps_img"]
std = solution["sd_img"]
tms = solution["itime_img"]
for i_solution in xrange(1,len(all_solutions)):
info("Combining solution %i" %i_solution)
solution = all_solutions[i_solution][i_slit]
img += solution["eps_img"]
std += solution["sd_img"]
tms += solution["itime_img"]
#print "adding in quadrature"
output = np.append(output, img, 0)
output = np.append(output, np.nan*np.zeros((3,S[1])), 0)
snrs = np.append(snrs, img*tms/std, 0)
snrs = np.append(snrs, np.nan*np.zeros((3,S[1])), 0)
sdout = np.append(sdout, std, 0)
sdout = np.append(sdout, np.nan*np.zeros((3,S[1])), 0)
itout = np.append(itout, tms, 0)
itout = np.append(itout, np.nan*np.zeros((3,S[1])), 0)
header['bunit'] = ('electron/second', 'electron power')
IO.writefits(img, maskname,
"{0}_{1}_{2}_eps.fits".format(outname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('electron/second', 'sigma/itime')
IO.writefits(std/tms, maskname,
"{0}_{1}_{2}_sig.fits".format(outname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('second', 'exposure time')
IO.writefits(tms, maskname,
"{0}_{1}_{2}_itime.fits".format(outname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header['bunit'] = ('', 'SNR')
IO.writefits(img*tms/std, maskname,
"{0}_{1}_{2}_snrs.fits".format(outname, band, target_name), options,
overwrite=True, header=header, lossy_compress=False)
header = EPS[0].copy()
header["wat0_001"] = "system=world"
header["wat1_001"] = "wtype=linear"
header["wat2_001"] = "wtype=linear"
header["dispaxis"] = 1
header["dclog1"] = "Transform"
header["dc-flag"] = 0
header["ctype1"] = "AWAV"
header["cunit1"] = ("Angstrom", 'Start wavelength')
header["crval1"] = ll[0]
header["crval2"] = 1
header["crpix1"] = 1
header["crpix2"] = 1
#remove redundant CDELTi due to wavelength issues with ds9
#see: https://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/44
#header["cdelt1"] = 1
#header["cdelt2"] = 1
header["cname1"] = "angstrom"
header["cname2"] = "pixel"
header["cd1_1"] = (ll[1]-ll[0], 'Angstrom/pixel')
header["cd1_2"] = 0
header["cd2_1"] = 0
header["cd2_2"] = 1
try:
header["BARYCORR"]= (lambdas[0]['BARYCORR'],lambdas[0].comments['BARYCORR'])
except KeyError:
warning( "Barycentric corrections not applied to the wavelength solution")
pass
header["bunit"] = "ELECTRONS/SECOND"
info("############ Final reduced file: {0}_{1}_eps.fits".format(outname,band))
IO.writefits(output, maskname, "{0}_{1}_eps.fits".format(outname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = ""
IO.writefits(snrs, maskname, "{0}_{1}_snrs.fits".format(outname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = "ELECTRONS/SECOND"
IO.writefits(sdout/itout, maskname, "{0}_{1}_sig.fits".format(outname,
band), options, overwrite=True, header=header,
lossy_compress=False)
header["bunit"] = "SECOND"
IO.writefits(itout, maskname, "{0}_{1}_itime.fits".format(outname,
band), options, overwrite=True, header=header,
lossy_compress=False)
import pyfits as pf np.seterr(all='ignore') flatops = Options.flat waveops = Options.wavelength #Driver file automatically generated on Sat Jul 25 17:33:42 2015 #For questions and comments, email [email protected], submit a ticket on the ticketing system, or contact Luca Rizzi @ WMKO maskname = 'maskname' band = 'band' #Set noninteractive to True to autofit wavelenth solution instead of manually fitting. noninteractiveflag=False obsfiles=['Offset_1.25.txt','Offset_-1.25.txt'] Flats.handle_flats('Flat.txt', maskname, band, flatops) Wavelength.imcombine(obsfiles, maskname, band, waveops) Wavelength.fit_lambda_interactively(maskname, band, obsfiles,waveops, noninteractive=noninteractiveflag) Wavelength.fit_lambda(maskname, band, obsfiles, obsfiles,waveops) Wavelength.apply_lambda_simple(maskname, band, obsfiles, waveops) # modify this variable to point to the correct wavelength file created on the previous step Wavelength_file = 'lambda_solution_wave_stack_H_m141130_0323-0338.fits' Background.handle_background(obsfiles,Wavelength_file,maskname,band,waveops) redfiles = ["eps_" + file + ".fits" for file in obsfiles] Rectify.handle_rectification(maskname, redfiles,Wavelength_file,band,obsfiles,waveops)
longslit = {"yrange": [[1062, 1188], [887, 1010]], "row_position": 0, "mode": "long2pos"}
Flats.handle_flats("Flat.txt", maskname, band, flatops, longslit=longslit)
# in this case, we are using the argon lines.
# replace this with neon=['Ne.txt'] if you prefer to use Ne, and edit the following lines accordingly
argon = ["Ar.txt"]
Wavelength.imcombine(argon, maskname, band, waveops)
Wavelength.fit_lambda_interactively(maskname, band, argon, waveops, longslit=longslit, argon=True, bypass=bypassflag)
Wavelength.fit_lambda(maskname, band, argon, argon, waveops, longslit=longslit)
Wavelength.apply_lambda_simple(maskname, band, argon, waveops, longslit=longslit, smooth=True)
# make sure you use the correct wavelength file generated before
Wavelength_file = "lambda_solution_wave_stack_H_m150428_0091-0091.fits"
# narrow
Background.handle_background(obsfiles_posAnarrow, Wavelength_file, maskname, band, waveops, target=target_posAnarrow)
Background.handle_background(obsfiles_posCnarrow, Wavelength_file, maskname, band, waveops, target=target_posCnarrow)
# wide
Background.handle_background(obsfiles_posAwide, Wavelength_file, maskname, band, waveops, target=target_posAwide)
Background.handle_background(obsfiles_posCwide, Wavelength_file, maskname, band, waveops, target=target_posCwide)
# narrow
redfiles = ["eps_" + file + ".fits" for file in obsfiles_posAnarrow]
Rectify.handle_rectification(
maskname, redfiles, Wavelength_file, band, obsfiles_posAnarrow, waveops, target=target_posAnarrow
)
redfiles = ["eps_" + file + ".fits" for file in obsfiles_posCnarrow]
Rectify.handle_rectification(
maskname, redfiles, Wavelength_file, band, obsfiles_posCnarrow, waveops, target=target_posCnarrow
)
# wide
# Change the bad pixel mask path
# Options.path_bpm = "/scr2/mosfire/badpixels/badpix_18may2012.fits"
# Change if False to if True when you want to execute that step
# On interactive step, make sure you attempt to quit&save after fitting one
# slit!
if False: Flats.handle_flats(flatnames, maskname, band, flatops)
if False: Wavelength.imcombine(wavenames1, maskname, band, wavlops)
if False: Wavelength.imcombine(wavenames2, maskname, band, wavlops)
# only one interactive fit is needed
if False: Wavelength.fit_lambda_interactively(maskname, band, wavenames1,
wavlops)
# mask band to fit guess options
if False: Wavelength.fit_lambda(maskname, band, wavenames1, wavenames1, wavlops)
if False: Wavelength.fit_lambda(maskname, band, wavenames2, wavenames1, wavlops)
if False: Wavelength.apply_lambda_simple(maskname, band, wavenames1, wavlops)
if False: Wavelength.apply_lambda_simple(maskname, band, wavenames2, wavlops)
As = As1[:]
Bs = Bs1[:]
As.extend(As2)
Bs.extend(Bs2)
if True: Background.handle_background(As, Bs, wavenames1, maskname, band, wavlops)
if True: Rectify.handle_rectification(maskname, ["A", "B"], wavenames1, band,
wavlops)