def test_check_filters(self):
filterlist = [
'SDSS_U', 'SDSS_G', 'SDSS_R', 'SDSS_I', 'SDSS_Z', 'DECAM_U',
'DECAM_G', 'DECAM_R', 'DECAM_I', 'DECAM_Z', 'DECAM_Y', 'WISE_W1',
'WISE_W2'
]
filters = ['XXXX', 'YYYY', 'ZZZZ']
stdwave = np.linspace(3000, 11000, 10000)
stdflux = np.cos(stdwave) + 100.
mags = np.array([20, 21, 22])
# No correct filters
with self.assertRaises(SystemExit):
normflux = normalize_templates(stdwave, stdflux, mags, filters)
filters = filters + ['DECAM_R']
#This should use DECAM_R for calibration
mags = np.concatenate([mags, np.array([23])])
normflux = normalize_templates(stdwave, stdflux, mags, filters)
r = speclite.filters.load_filter('decam2014-r')
rmag = r.get_ab_magnitude(1e-17 * normflux, stdwave)
self.assertAlmostEqual(rmag, mags[-1])
#check dimensionality
self.assertEqual(stdflux.shape, normflux.shape)
def test_check_filters(self):
filterlist=['SDSS_U','SDSS_G','SDSS_R','SDSS_I','SDSS_Z','DECAM_U','DECAM_G','DECAM_R',
'DECAM_I','DECAM_Z','DECAM_Y','WISE_W1','WISE_W2']
filters=['XXXX','YYYY','ZZZZ']
stdwave=np.linspace(3000,11000,10000)
stdflux=np.cos(stdwave)+100.
mags=np.array([20,21,22])
# No correct filters
with self.assertRaises(SystemExit):
normflux=normalize_templates(stdwave,stdflux,mags,filters)
filters=filters+['DECAM_R']
#This should use DECAM_R for calibration
mags=np.concatenate([mags,np.array([23])])
normflux=normalize_templates(stdwave,stdflux,mags,filters)
r = speclite.filters.load_filter('decam2014-r')
rmag = r.get_ab_magnitude(1e-17*normflux, stdwave)
self.assertAlmostEqual(rmag, mags[-1])
#check dimensionality
self.assertEqual(stdflux.shape, normflux.shape)
def test_normalize_templates(self):
"""
Test for normalization to a given magnitude for calibration
"""
stdwave=np.linspace(3000,11000,10000)
stdflux=np.cos(stdwave)+100.
mag = 20.0
normflux=normalize_templates(stdwave,stdflux,mag,'DECAM_R')
self.assertEqual(stdflux.shape, normflux.shape)
r = speclite.filters.load_filter('decam2014-r')
rmag = r.get_ab_magnitude(1e-17*normflux, stdwave)
self.assertAlmostEqual(rmag, mag)
def test_normalize_templates(self):
"""
Test for normalization to a given magnitude for calibration
"""
stdwave = np.linspace(3000, 11000, 10000)
stdflux = np.cos(stdwave) + 100.
mag = 20.0
normflux = normalize_templates(stdwave, stdflux, mag, 'DECAM_R')
self.assertEqual(stdflux.shape, normflux.shape)
r = speclite.filters.load_filter('decam2014-r')
rmag = r.get_ab_magnitude(1e-17 * normflux, stdwave)
self.assertAlmostEqual(rmag, mag)
def test_normalize_templates(self):
"""
Test for normalization to a given magnitude for calibration
"""
stdwave=np.linspace(3000,11000,10000)
stdflux=np.cos(stdwave)+100.
mag = 20.0
normflux=normalize_templates(stdwave,stdflux,mag,'R','S')
self.assertEqual(stdflux.shape, normflux.shape)
r = load_legacy_survey_filter('R','S')
rmag = r.get_ab_magnitude(1e-17*normflux, stdwave)
self.assertAlmostEqual(rmag, mag)
def test_normalize_templates(self):
"""
Test for normalization to a given magnitude for calibration
"""
stdwave=np.linspace(3000,11000,10000)
stdflux=np.cos(stdwave)+100.
mags=np.array((20,21))
filters=['SDSS_I','SDSS_R']
#This should use SDSS_R for calibration
normflux=normalize_templates(stdwave,stdflux,mags,filters)
self.assertEqual(stdflux.shape, normflux.shape)
r = speclite.filters.load_filter('sdss2010-r')
rmag = r.get_ab_magnitude(1e-17*normflux, stdwave)
self.assertAlmostEqual(rmag, mags[1])
def test_normalize_templates(self):
"""
Test for normalization to a given magnitude for calibration
"""
stdwave=np.linspace(3000,11000,10000)
stdflux=np.cos(stdwave)+100.
mags=np.array((20,21))
filters=['SDSS_I','SDSS_R']
#This should use SDSS_R for calibration
normflux=normalize_templates(stdwave,stdflux,mags,filters)
self.assertEqual(stdflux.shape, normflux.shape)
r = speclite.filters.load_filter('sdss2010-r')
rmag = r.get_ab_magnitude(1e-17*normflux, stdwave)
self.assertAlmostEqual(rmag, mags[1])
def main() :
""" finds the best models of all standard stars in the frame
and normlize the model flux. Output is written to a file and will be called for calibration.
"""
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--fiberflatexpid', type = int, help = 'fiberflat exposure ID')
parser.add_argument('--fibermap', type = str, help = 'path of fibermap file')
parser.add_argument('--models', type = str, help = 'path of spectro-photometric stellar spectra fits')
parser.add_argument('--spectrograph', type = int, default = 0, help = 'spectrograph number, can go 0-9')
parser.add_argument('--outfile', type = str, help = 'output file for normalized stdstar model flux')
args = parser.parse_args()
log = get_logger()
# Call necessary environment variables. No need if add argument to give full file path.
if 'DESI_SPECTRO_REDUX' not in os.environ:
raise RuntimeError('Set environment DESI_SPECTRO_REDUX. It is needed to read the needed datafiles')
DESI_SPECTRO_REDUX=os.environ['DESI_SPECTRO_REDUX']
PRODNAME=os.environ['PRODNAME']
if 'DESISIM' not in os.environ:
raise RuntimeError('Set environment DESISIM. It will be neede to read the filter transmission files for calibration')
DESISIM=os.environ['DESISIM'] # to read the filter transmission files
if args.fibermap is None or args.models is None or \
args.spectrograph is None or args.outfile is None or \
args.fiberflatexpid is None:
log.critical('Missing a required argument')
parser.print_help()
sys.exit(12)
# read Standard Stars from the fibermap file
# returns the Fiber id, filter names and mags for the standard stars
fiber_tbdata,fiber_header=io.read_fibermap(args.fibermap, header=True)
#- Trim to just fibers on this spectrograph
ii = (500*args.spectrograph <= fiber_tbdata["FIBER"])
ii &= (fiber_tbdata["FIBER"] < 500*(args.spectrograph+1))
fiber_tbdata = fiber_tbdata[ii]
#- Get info for the standard stars
refStarIdx=np.where(fiber_tbdata["OBJTYPE"]=="STD")
refFibers=fiber_tbdata["FIBER"][refStarIdx]
refFilters=fiber_tbdata["FILTER"][refStarIdx]
refMags=fiber_tbdata["MAG"]
fibers={"FIBER":refFibers,"FILTER":refFilters,"MAG":refMags}
NIGHT=fiber_header['NIGHT']
EXPID=fiber_header['EXPID']
filters=fibers["FILTER"]
if 'DESISIM' not in os.environ:
raise RuntimeError('Set environment DESISIM. Can not find filter response files')
basepath=DESISIM+"/data/"
#now load all the skyfiles, framefiles, fiberflatfiles etc
# all three channels files are simultaneously treated for model fitting
skyfile={}
framefile={}
fiberflatfile={}
for i in ["b","r","z"]:
camera = i+str(args.spectrograph)
skyfile[i] = io.findfile('sky', NIGHT, EXPID, camera)
framefile[i] = io.findfile('frame', NIGHT, EXPID, camera)
fiberflatfile[i] = io.findfile('fiberflat', NIGHT, args.fiberflatexpid, camera)
#Read Frames, Flats and Sky files
frameFlux={}
frameIvar={}
frameWave={}
frameResolution={}
framehdr={}
fiberFlat={}
ivarFlat={}
maskFlat={}
meanspecFlat={}
waveFlat={}
headerFlat={}
sky={}
skyivar={}
skymask={}
skywave={}
skyhdr={}
for i in ["b","r","z"]:
#arg=(night,expid,'%s%s'%(i,spectrograph))
#- minimal code change for refactored I/O, while not taking advantage of simplified structure
frame = io.read_frame(framefile[i])
frameFlux[i] = frame.flux
frameIvar[i] = frame.ivar
frameWave[i] = frame.wave
frameResolution[i] = frame.resolution_data
framehdr[i] = frame.header
ff = io.read_fiberflat(fiberflatfile[i])
fiberFlat[i] = ff.fiberflat
ivarFlat[i] = ff.ivar
maskFlat[i] = ff.mask
meanspecFlat[i] = ff.meanspec
waveFlat[i] = ff.wave
headerFlat[i] = ff.header
skymodel = io.read_sky(skyfile[i])
sky[i] = skymodel.flux
skyivar[i] = skymodel.ivar
skymask[i] = skymodel.mask
skywave[i] = skymodel.wave
skyhdr[i] = skymodel.header
# Convolve Sky with Detector Resolution, so as to subtract from data. Convolve for all 500 specs. Subtracting sky this way should be equivalent to sky_subtract
convolvedsky={"b":sky["b"], "r":sky["r"], "z":sky["z"]}
# Read the standard Star data and divide by flat and subtract sky
stars=[]
ivars=[]
for i in fibers["FIBER"]:
#flat and sky should have same wavelength binning as data, otherwise should be rebinned.
stars.append((i,{"b":[frameFlux["b"][i]/fiberFlat["b"][i]-convolvedsky["b"][i],frameWave["b"]],
"r":[frameFlux["r"][i]/fiberFlat["r"][i]-convolvedsky["r"][i],frameWave["r"]],
"z":[frameFlux["z"][i]/fiberFlat["z"][i]-convolvedsky["z"][i],frameWave]},fibers["MAG"][i]))
ivars.append((i,{"b":[frameIvar["b"][i]],"r":[frameIvar["r"][i,:]],"z":[frameIvar["z"][i,:]]}))
stdwave,stdflux,templateid=io.read_stdstar_templates(args.models)
#- Trim standard star wavelengths to just the range we need
minwave = min([min(w) for w in frameWave.values()])
maxwave = max([max(w) for w in frameWave.values()])
ii = (minwave-10 < stdwave) & (stdwave < maxwave+10)
stdwave = stdwave[ii]
stdflux = stdflux[:, ii]
log.info('Number of Standard Stars in this frame: {0:d}'.format(len(stars)))
if len(stars) == 0:
log.critical("No standard stars! Exiting")
sys.exit(1)
# Now for each star, find the best model and normalize.
normflux=[]
bestModelIndex=np.arange(len(stars))
templateID=np.arange(len(stars))
chi2dof=np.zeros(len(stars))
#- TODO: don't use 'l' as a variable name. Can look like a '1'
for k,l in enumerate(stars):
log.info("checking best model for star {0}".format(l[0]))
starindex=l[0]
mags=l[2]
filters=fibers["FILTER"][k]
rflux=stars[k][1]["r"][0]
bflux=stars[k][1]["b"][0]
zflux=stars[k][1]["z"][0]
flux={"b":bflux,"r":rflux,"z":zflux}
#print ivars
rivar=ivars[k][1]["r"][0]
bivar=ivars[k][1]["b"][0]
zivar=ivars[k][1]["z"][0]
ivar={"b":bivar,"r":rivar,"z":zivar}
resol_star={"r":frameResolution["r"][l[0]],"b":frameResolution["b"][l[0]],"z":frameResolution["z"][l[0]]}
# Now find the best Model
bestModelIndex[k],bestmodelWave,bestModelFlux,chi2dof[k]=match_templates(frameWave,flux,ivar,resol_star,stdwave,stdflux)
log.info('Star Fiber: {0}; Best Model Fiber: {1}; TemplateID: {2}; Chisq/dof: {3}'.format(l[0],bestModelIndex[k],templateid[bestModelIndex[k]],chi2dof[k]))
# Normalize the best model using reported magnitude
modelwave,normalizedflux=normalize_templates(stdwave,stdflux[bestModelIndex[k]],mags,filters,basepath)
normflux.append(normalizedflux)
# Now write the normalized flux for all best models to a file
normflux=np.array(normflux)
stdfibers=fibers["FIBER"]
data={}
data['BESTMODEL']=bestModelIndex
data['CHI2DOF']=chi2dof
data['TEMPLATEID']=templateid[bestModelIndex]
norm_model_file=args.outfile
io.write_stdstar_model(norm_model_file,normflux,stdwave,stdfibers,data)
def main(args):
""" finds the best models of all standard stars in the frame
and normlize the model flux. Output is written to a file and will be called for calibration.
"""
log = get_logger()
log.info("mag delta %s = %f (for the pre-selection of stellar models)" %
(args.color, args.delta_color))
frames = {}
flats = {}
skies = {}
spectrograph = None
starfibers = None
starindices = None
fibermap = None
# READ DATA
############################################
for filename in args.frames:
log.info("reading %s" % filename)
frame = io.read_frame(filename)
header = fits.getheader(filename, 0)
frame_fibermap = frame.fibermap
frame_starindices = np.where(frame_fibermap["OBJTYPE"] == "STD")[0]
camera = safe_read_key(header, "CAMERA").strip().lower()
if spectrograph is None:
spectrograph = frame.spectrograph
fibermap = frame_fibermap
starindices = frame_starindices
starfibers = fibermap["FIBER"][starindices]
elif spectrograph != frame.spectrograph:
log.error("incompatible spectrographs %d != %d" %
(spectrograph, frame.spectrograph))
raise ValueError("incompatible spectrographs %d != %d" %
(spectrograph, frame.spectrograph))
elif starindices.size != frame_starindices.size or np.sum(
starindices != frame_starindices) > 0:
log.error("incompatible fibermap")
raise ValueError("incompatible fibermap")
if frames.has_key(camera):
log.error(
"cannot handle for now several frame of same camera (%s)" %
camera)
raise ValueError(
"cannot handle for now several frame of same camera (%s)" %
camera)
frames[camera] = frame
for filename in args.skymodels:
log.info("reading %s" % filename)
sky = io.read_sky(filename)
header = fits.getheader(filename, 0)
camera = safe_read_key(header, "CAMERA").strip().lower()
# NEED TO ADD MORE CHECKS
if skies.has_key(camera):
log.error("cannot handle several skymodels of same camera (%s)" %
camera)
raise ValueError(
"cannot handle several skymodels of same camera (%s)" % camera)
skies[camera] = sky
for filename in args.fiberflats:
log.info("reading %s" % filename)
header = fits.getheader(filename, 0)
flat = io.read_fiberflat(filename)
camera = safe_read_key(header, "CAMERA").strip().lower()
# NEED TO ADD MORE CHECKS
if flats.has_key(camera):
log.error("cannot handle several flats of same camera (%s)" %
camera)
raise ValueError(
"cannot handle several flats of same camera (%s)" % camera)
flats[camera] = flat
if starindices.size == 0:
log.error("no STD star found in fibermap")
raise ValueError("no STD star found in fibermap")
log.info("found %d STD stars" % starindices.size)
imaging_filters = fibermap["FILTER"][starindices]
imaging_mags = fibermap["MAG"][starindices]
log.warning(
"NO MAG ERRORS IN FIBERMAP, I AM IGNORING MEASUREMENT ERRORS !!")
log.warning(
"NO EXTINCTION VALUES IN FIBERMAP, I AM IGNORING THIS FOR NOW !!")
# DIVIDE FLAT AND SUBTRACT SKY , TRIM DATA
############################################
for cam in frames:
if not skies.has_key(cam):
log.warning("Missing sky for %s" % cam)
frames.pop(cam)
continue
if not flats.has_key(cam):
log.warning("Missing flat for %s" % cam)
frames.pop(cam)
continue
frames[cam].flux = frames[cam].flux[starindices]
frames[cam].ivar = frames[cam].ivar[starindices]
frames[cam].ivar *= (frames[cam].mask[starindices] == 0)
frames[cam].ivar *= (skies[cam].ivar[starindices] != 0)
frames[cam].ivar *= (skies[cam].mask[starindices] == 0)
frames[cam].ivar *= (flats[cam].ivar[starindices] != 0)
frames[cam].ivar *= (flats[cam].mask[starindices] == 0)
frames[cam].flux *= (frames[cam].ivar > 0) # just for clean plots
for star in range(frames[cam].flux.shape[0]):
ok = np.where((frames[cam].ivar[star] > 0)
& (flats[cam].fiberflat[star] != 0))[0]
if ok.size > 0:
frames[cam].flux[star] = frames[cam].flux[star] / flats[
cam].fiberflat[star] - skies[cam].flux[star]
nstars = starindices.size
starindices = None # we don't need this anymore
# READ MODELS
############################################
log.info("reading star models in %s" % args.starmodels)
stdwave, stdflux, templateid, teff, logg, feh = io.read_stdstar_templates(
args.starmodels)
# COMPUTE MAGS OF MODELS FOR EACH STD STAR MAG
############################################
model_filters = []
for tmp in np.unique(imaging_filters):
if len(tmp) > 0: # can be one empty entry
model_filters.append(tmp)
log.info("computing model mags %s" % model_filters)
model_mags = np.zeros((stdflux.shape[0], len(model_filters)))
fluxunits = 1e-17 * units.erg / units.s / units.cm**2 / units.Angstrom
for index in range(len(model_filters)):
filter_response = load_filter(model_filters[index])
for m in range(stdflux.shape[0]):
model_mags[m, index] = filter_response.get_ab_magnitude(
stdflux[m] * fluxunits, stdwave)
log.info("done computing model mags")
# LOOP ON STARS TO FIND BEST MODEL
############################################
bestModelIndex = np.arange(nstars)
templateID = np.arange(nstars)
chi2dof = np.zeros((nstars))
redshift = np.zeros((nstars))
normflux = []
for star in range(nstars):
log.info("finding best model for observed star #%d" % star)
# np.array of wave,flux,ivar,resol
wave = {}
flux = {}
ivar = {}
resolution_data = {}
for camera in frames:
band = camera[0]
wave[band] = frames[camera].wave
flux[band] = frames[camera].flux[star]
ivar[band] = frames[camera].ivar[star]
resolution_data[band] = frames[camera].resolution_data[star]
# preselec models based on magnitudes
# compute star color
index1, index2 = get_color_filter_indices(imaging_filters[star],
args.color)
if index1 < 0 or index2 < 0:
log.error("cannot compute '%s' color from %s" %
(color_name, filters))
filter1 = imaging_filters[star][index1]
filter2 = imaging_filters[star][index2]
star_color = imaging_mags[star][index1] - imaging_mags[star][index2]
# compute models color
model_index1 = -1
model_index2 = -1
for i, fname in enumerate(model_filters):
if fname == filter1:
model_index1 = i
elif fname == filter2:
model_index2 = i
if model_index1 < 0 or model_index2 < 0:
log.error("cannot compute '%s' model color from %s" %
(color_name, filters))
model_colors = model_mags[:, model_index1] - model_mags[:,
model_index2]
# selection
selection = np.where(
np.abs(model_colors - star_color) < args.delta_color)[0]
log.info(
"star#%d fiber #%d, %s = %s-%s = %f, number of pre-selected models = %d/%d"
% (star, starfibers[star], args.color, filter1, filter2,
star_color, selection.size, stdflux.shape[0]))
index_in_selection, redshift[star], chi2dof[star] = match_templates(
wave,
flux,
ivar,
resolution_data,
stdwave,
stdflux[selection],
teff[selection],
logg[selection],
feh[selection],
ncpu=args.ncpu,
z_max=args.z_max,
z_res=args.z_res)
bestModelIndex[star] = selection[index_in_selection]
log.info(
'Star Fiber: {0}; TemplateID: {1}; Redshift: {2}; Chisq/dof: {3}'.
format(starfibers[star], bestModelIndex[star], redshift[star],
chi2dof[star]))
# Apply redshift to original spectrum at full resolution
tmp = np.interp(stdwave, stdwave / (1 + redshift[star]),
stdflux[bestModelIndex[star]])
# Normalize the best model using reported magnitude
normalizedflux = normalize_templates(stdwave, tmp, imaging_mags[star],
imaging_filters[star])
normflux.append(normalizedflux)
# Now write the normalized flux for all best models to a file
normflux = np.array(normflux)
data = {}
data['BESTMODEL'] = bestModelIndex
data['TEMPLATEID'] = bestModelIndex # IS THAT IT?
data['CHI2DOF'] = chi2dof
data['REDSHIFT'] = redshift
norm_model_file = args.outfile
io.write_stdstar_models(args.outfile, normflux, stdwave, starfibers, data)
def main(args):
""" finds the best models of all standard stars in the frame
and normlize the model flux. Output is written to a file and will be called for calibration.
"""
log = get_logger()
log.info("mag delta %s = %f (for the pre-selection of stellar models)" %
(args.color, args.delta_color))
frames = {}
flats = {}
skies = {}
spectrograph = None
starfibers = None
starindices = None
fibermap = None
# READ DATA
############################################
for filename in args.frames:
log.info("reading %s" % filename)
frame = io.read_frame(filename)
header = fits.getheader(filename, 0)
frame_fibermap = frame.fibermap
frame_starindices = np.where(frame_fibermap["OBJTYPE"] == "STD")[0]
# check magnitude are well defined or discard stars
tmp = []
for i in frame_starindices:
mags = frame_fibermap["MAG"][i]
ok = np.sum((mags > 0) & (mags < 30))
if np.sum((mags > 0) & (mags < 30)) == mags.size:
tmp.append(i)
frame_starindices = np.array(tmp).astype(int)
camera = safe_read_key(header, "CAMERA").strip().lower()
if spectrograph is None:
spectrograph = frame.spectrograph
fibermap = frame_fibermap
starindices = frame_starindices
starfibers = fibermap["FIBER"][starindices]
elif spectrograph != frame.spectrograph:
log.error("incompatible spectrographs %d != %d" %
(spectrograph, frame.spectrograph))
raise ValueError("incompatible spectrographs %d != %d" %
(spectrograph, frame.spectrograph))
elif starindices.size != frame_starindices.size or np.sum(
starindices != frame_starindices) > 0:
log.error("incompatible fibermap")
raise ValueError("incompatible fibermap")
if not camera in frames:
frames[camera] = []
frames[camera].append(frame)
for filename in args.skymodels:
log.info("reading %s" % filename)
sky = io.read_sky(filename)
header = fits.getheader(filename, 0)
camera = safe_read_key(header, "CAMERA").strip().lower()
if not camera in skies:
skies[camera] = []
skies[camera].append(sky)
for filename in args.fiberflats:
log.info("reading %s" % filename)
header = fits.getheader(filename, 0)
flat = io.read_fiberflat(filename)
camera = safe_read_key(header, "CAMERA").strip().lower()
# NEED TO ADD MORE CHECKS
if camera in flats:
log.warning(
"cannot handle several flats of same camera (%s), will use only the first one"
% camera)
#raise ValueError("cannot handle several flats of same camera (%s)"%camera)
else:
flats[camera] = flat
if starindices.size == 0:
log.error("no STD star found in fibermap")
raise ValueError("no STD star found in fibermap")
log.info("found %d STD stars" % starindices.size)
imaging_filters = fibermap["FILTER"][starindices]
imaging_mags = fibermap["MAG"][starindices]
log.warning(
"NO MAG ERRORS IN FIBERMAP, I AM IGNORING MEASUREMENT ERRORS !!")
ebv = np.zeros(starindices.size)
if "SFD_EBV" in fibermap.columns.names:
log.info("Using 'SFD_EBV' from fibermap")
ebv = fibermap["SFD_EBV"][starindices]
else:
log.warning("NO EXTINCTION VALUES IN FIBERMAP!!")
# DIVIDE FLAT AND SUBTRACT SKY , TRIM DATA
############################################
for cam in frames:
if not cam in skies:
log.warning("Missing sky for %s" % cam)
frames.pop(cam)
continue
if not cam in flats:
log.warning("Missing flat for %s" % cam)
frames.pop(cam)
continue
flat = flats[cam]
for frame, sky in zip(frames[cam], skies[cam]):
frame.flux = frame.flux[starindices]
frame.ivar = frame.ivar[starindices]
frame.ivar *= (frame.mask[starindices] == 0)
frame.ivar *= (sky.ivar[starindices] != 0)
frame.ivar *= (sky.mask[starindices] == 0)
frame.ivar *= (flat.ivar[starindices] != 0)
frame.ivar *= (flat.mask[starindices] == 0)
frame.flux *= (frame.ivar > 0) # just for clean plots
for star in range(frame.flux.shape[0]):
ok = np.where((frame.ivar[star] > 0)
& (flat.fiberflat[star] != 0))[0]
if ok.size > 0:
frame.flux[star] = frame.flux[star] / flat.fiberflat[
star] - sky.flux[star]
frame.resolution_data = frame.resolution_data[starindices]
nstars = starindices.size
starindices = None # we don't need this anymore
# READ MODELS
############################################
log.info("reading star models in %s" % args.starmodels)
stdwave, stdflux, templateid, teff, logg, feh = io.read_stdstar_templates(
args.starmodels)
# COMPUTE MAGS OF MODELS FOR EACH STD STAR MAG
############################################
model_filters = []
for tmp in np.unique(imaging_filters):
if len(tmp) > 0: # can be one empty entry
model_filters.append(tmp)
log.info("computing model mags %s" % model_filters)
model_mags = np.zeros((stdflux.shape[0], len(model_filters)))
fluxunits = 1e-17 * units.erg / units.s / units.cm**2 / units.Angstrom
for index in range(len(model_filters)):
if model_filters[index].startswith('WISE'):
log.warning('not computing stdstar {} mags'.format(
model_filters[index]))
continue
filter_response = load_filter(model_filters[index])
for m in range(stdflux.shape[0]):
model_mags[m, index] = filter_response.get_ab_magnitude(
stdflux[m] * fluxunits, stdwave)
log.info("done computing model mags")
mean_extinction_delta_mags = None
mean_ebv = np.mean(ebv)
if mean_ebv > 0:
log.info(
"Compute a mean delta_color from average E(B-V) = %3.2f based on canonial model star"
% mean_ebv)
# compute a mean delta_color from mean_ebv based on canonial model star
#######################################################################
# will then use this color offset in the model pre-selection
# find canonical f-type model: Teff=6000, logg=4, Fe/H=-1.5
canonical_model = np.argmin((teff - 6000.0)**2 + (logg - 4.0)**2 +
(feh + 1.5)**2)
canonical_model_mags_without_extinction = model_mags[canonical_model]
canonical_model_mags_with_extinction = np.zeros(
canonical_model_mags_without_extinction.shape)
canonical_model_reddened_flux = stdflux[
canonical_model] * dust_transmission(stdwave, mean_ebv)
for index in range(len(model_filters)):
if model_filters[index].startswith('WISE'):
log.warning('not computing stdstar {} mags'.format(
model_filters[index]))
continue
filter_response = load_filter(model_filters[index])
canonical_model_mags_with_extinction[
index] = filter_response.get_ab_magnitude(
canonical_model_reddened_flux * fluxunits, stdwave)
mean_extinction_delta_mags = canonical_model_mags_with_extinction - canonical_model_mags_without_extinction
# LOOP ON STARS TO FIND BEST MODEL
############################################
linear_coefficients = np.zeros((nstars, stdflux.shape[0]))
chi2dof = np.zeros((nstars))
redshift = np.zeros((nstars))
normflux = []
star_colors_array = np.zeros((nstars))
model_colors_array = np.zeros((nstars))
for star in range(nstars):
log.info("finding best model for observed star #%d" % star)
# np.array of wave,flux,ivar,resol
wave = {}
flux = {}
ivar = {}
resolution_data = {}
for camera in frames:
for i, frame in enumerate(frames[camera]):
identifier = "%s-%d" % (camera, i)
wave[identifier] = frame.wave
flux[identifier] = frame.flux[star]
ivar[identifier] = frame.ivar[star]
resolution_data[identifier] = frame.resolution_data[star]
# preselec models based on magnitudes
# compute star color
index1, index2 = get_color_filter_indices(imaging_filters[star],
args.color)
if index1 < 0 or index2 < 0:
log.error("cannot compute '%s' color from %s" %
(color_name, filters))
filter1 = imaging_filters[star][index1]
filter2 = imaging_filters[star][index2]
star_color = imaging_mags[star][index1] - imaging_mags[star][index2]
star_colors_array[star] = star_color
# compute models color
model_index1 = -1
model_index2 = -1
for i, fname in enumerate(model_filters):
if fname == filter1:
model_index1 = i
elif fname == filter2:
model_index2 = i
if model_index1 < 0 or model_index2 < 0:
log.error("cannot compute '%s' model color from %s" %
(color_name, filters))
model_colors = model_mags[:, model_index1] - model_mags[:,
model_index2]
# apply extinction here
# use the colors derived from the cannonical model with the mean ebv of the stars
# and simply apply a scaling factor based on the ebv of this star
# this is sufficiently precise for the broad model pre-selection we are doing here
# the exact reddening of the star to each pre-selected model is
# apply afterwards
if mean_extinction_delta_mags is not None and mean_ebv != 0:
delta_color = (mean_extinction_delta_mags[model_index1] -
mean_extinction_delta_mags[model_index2]
) * ebv[star] / mean_ebv
model_colors += delta_color
log.info(
"Apply a %s-%s color offset = %4.3f to the models for star with E(B-V)=%4.3f"
% (model_filters[model_index1], model_filters[model_index2],
delta_color, ebv[star]))
# selection
selection = np.abs(model_colors - star_color) < args.delta_color
# smallest cube in parameter space including this selection (needed for interpolation)
new_selection = (teff >= np.min(teff[selection])) & (teff <= np.max(
teff[selection]))
new_selection &= (logg >= np.min(logg[selection])) & (logg <= np.max(
logg[selection]))
new_selection &= (feh >= np.min(feh[selection])) & (feh <= np.max(
feh[selection]))
selection = np.where(new_selection)[0]
log.info(
"star#%d fiber #%d, %s = %s-%s = %f, number of pre-selected models = %d/%d"
% (star, starfibers[star], args.color, filter1, filter2,
star_color, selection.size, stdflux.shape[0]))
# apply extinction to selected_models
dust_transmission_of_this_star = dust_transmission(stdwave, ebv[star])
selected_reddened_stdflux = stdflux[
selection] * dust_transmission_of_this_star
coefficients, redshift[star], chi2dof[star] = match_templates(
wave,
flux,
ivar,
resolution_data,
stdwave,
selected_reddened_stdflux,
teff[selection],
logg[selection],
feh[selection],
ncpu=args.ncpu,
z_max=args.z_max,
z_res=args.z_res,
template_error=args.template_error)
linear_coefficients[star, selection] = coefficients
log.info(
'Star Fiber: {0}; TEFF: {1}; LOGG: {2}; FEH: {3}; Redshift: {4}; Chisq/dof: {5}'
.format(starfibers[star], np.inner(teff,
linear_coefficients[star]),
np.inner(logg, linear_coefficients[star]),
np.inner(feh, linear_coefficients[star]), redshift[star],
chi2dof[star]))
# Apply redshift to original spectrum at full resolution
model = np.zeros(stdwave.size)
for i, c in enumerate(linear_coefficients[star]):
if c != 0:
model += c * np.interp(stdwave, stdwave *
(1 + redshift[star]), stdflux[i])
# Apply dust extinction
model *= dust_transmission_of_this_star
# Compute final model color
mag1 = load_filter(model_filters[model_index1]).get_ab_magnitude(
model * fluxunits, stdwave)
mag2 = load_filter(model_filters[model_index2]).get_ab_magnitude(
model * fluxunits, stdwave)
model_colors_array[star] = mag1 - mag2
# Normalize the best model using reported magnitude
normalizedflux = normalize_templates(stdwave, model,
imaging_mags[star],
imaging_filters[star])
normflux.append(normalizedflux)
# Now write the normalized flux for all best models to a file
normflux = np.array(normflux)
data = {}
data['LOGG'] = linear_coefficients.dot(logg)
data['TEFF'] = linear_coefficients.dot(teff)
data['FEH'] = linear_coefficients.dot(feh)
data['CHI2DOF'] = chi2dof
data['REDSHIFT'] = redshift
data['COEFF'] = linear_coefficients
data['DATA_%s' % args.color] = star_colors_array
data['MODEL_%s' % args.color] = model_colors_array
norm_model_file = args.outfile
io.write_stdstar_models(args.outfile, normflux, stdwave, starfibers, data)
