def _write_flat_files(self):
# Frames
fb0 = self._make_frame(camera='b0', flavor='flat', nspec=10, objtype='FLAT')
_ = write_frame(self.frame_b0, fb0)
fb1 = self._make_frame(camera='b1', flavor='flat', nspec=10, objtype='FLAT')
_ = write_frame(self.frame_b1, fb1)
# Fiberflats
ff0 = get_fiberflat_from_frame(fb0)
write_fiberflat(self.fflat_b0, ff0)
ff1 = get_fiberflat_from_frame(fb1)
write_fiberflat(self.fflat_b1, ff1)
def run_pa(self,
input_image,
psf,
specmin,
nspec,
wave,
regularize=None,
ndecorr=True,
bundlesize=25,
wavesize=50,
outfile=None,
fibers=None,
fibermap=None):
import specter
from specter.extract import ex2d
from lvmspec.frame import Frame as fr
flux, ivar, Rdata = ex2d(input_image.pix,
input_image.ivar * (input_image.mask == 0),
psf,
specmin,
nspec,
wave,
regularize=regularize,
ndecorr=ndecorr,
bundlesize=bundlesize,
wavesize=wavesize)
#- Augment input image header for output
input_image.meta['NSPEC'] = (nspec, 'Number of spectra')
input_image.meta['WAVEMIN'] = (wave[0], 'First wavelength [Angstroms]')
input_image.meta['WAVEMAX'] = (wave[-1], 'Last wavelength [Angstroms]')
input_image.meta['WAVESTEP'] = (wave[1] - wave[0],
'Wavelength step size [Angstroms]')
input_image.meta['SPECTER'] = (specter.__version__,
'https://github.com/desihub/specter')
#input_image.meta['IN_PSF'] = (_trim(psf_file), 'Input spectral PSF')
#input_image.meta['IN_IMG'] = (_trim(input_file), 'Input image')
frame = fr(wave,
flux,
ivar,
resolution_data=Rdata,
fibers=fibers,
meta=input_image.meta,
fibermap=fibermap)
if outfile is not None: #- writing to a frame file if needed.
from lvmspec import io
io.write_frame(outfile, frame)
log.debug("wrote frame output file %s" % outfile)
return frame
def run_pa(self, input_frame, skymodel, dumpfile=None):
from lvmspec.quicklook.quicksky import subtract_sky
sframe = subtract_sky(input_frame, skymodel)
if dumpfile is not None:
from lvmspec import io
night = sframe.meta['NIGHT']
expid = sframe.meta['EXPID']
io.write_frame(dumpfile, sframe)
log.debug("Wrote intermediate file %s after %s" %
(dumpfile, self.name))
return (sframe, skymodel)
def run_pa(self, input_frame, fiberflat, dumpfile=None):
from lvmspec.quicklook.quickfiberflat import apply_fiberflat
fframe = apply_fiberflat(input_frame, fiberflat)
if dumpfile is not None:
from lvmspec import io
night = fframe.meta['NIGHT']
expid = fframe.meta['EXPID']
io.write_frame(dumpfile, fframe)
log.debug("Wrote intermediate file %s after %s" %
(dumpfile, self.name))
return fframe
def test_main(self):
"""
Test the main program.
"""
# generate the frame data
wave, flux, ivar, mask = _get_data()
nspec, nwave = flux.shape
#- Setup data for a Resolution matrix
sigma = 4.0
ndiag = 11
xx = np.linspace(-(ndiag - 1) / 2.0, +(ndiag - 1) / 2.0, ndiag)
Rdata = np.zeros((nspec, ndiag, nwave))
kernel = np.exp(-xx**2 / (2 * sigma))
kernel /= sum(kernel)
for i in range(nspec):
for j in range(nwave):
Rdata[i, :, j] = kernel
#- Convolve the data with the resolution matrix
convflux = np.empty_like(flux)
for i in range(nspec):
convflux[i] = Resolution(Rdata[i]).dot(flux[i])
# create a fake fibermap
fibermap = io.empty_fibermap(nspec, nwave)
for i in range(0, nspec):
fibermap['OBJTYPE'][i] = 'FAKE'
io.write_fibermap(self.testfibermap, fibermap)
#- write out the frame
frame = Frame(wave,
convflux,
ivar,
mask,
Rdata,
spectrograph=0,
fibermap=fibermap,
meta=dict(FLAVOR='flat'))
write_frame(self.testframe, frame, fibermap=fibermap)
# set program arguments
argstr = ['--infile', self.testframe, '--outfile', self.testflat]
# run it
args = ffscript.parse(options=argstr)
ffscript.main(args)
def main(args):
log = get_logger()
if (args.fiberflat is None) and (args.sky is None) and (args.calib is None):
log.critical('no --fiberflat, --sky, or --calib; nothing to do ?!?')
sys.exit(12)
frame = read_frame(args.infile)
if args.cosmics_nsig>0 : # Reject cosmics
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
if args.fiberflat!=None :
log.info("apply fiberflat")
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
if args.sky!=None :
log.info("subtract sky")
# read sky
skymodel=read_sky(args.sky)
# subtract sky
subtract_sky(frame, skymodel)
if args.calib!=None :
log.info("calibrate")
# read calibration
fluxcalib=read_flux_calibration(args.calib)
# apply calibration
apply_flux_calibration(frame, fluxcalib)
if args.cosmics_nsig>0 : # Reject cosmics one more time after sky subtraction to catch cosmics close to sky lines
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
# save output
write_frame(args.outfile, frame, units='1e-17 erg/(s cm2 A)')
log.info("successfully wrote %s"%args.outfile)
def _write_frame(self,
flavor='none',
camera='b',
expid=1,
night='20160607'):
"""Write a fake frame"""
flux = np.ones((self.nspec, self.nwave))
ivar = np.ones((self.nspec, self.nwave))
mask = np.zeros((self.nspec, self.nwave), dtype=int)
Rdata = np.ones((self.nspec, 1, self.nwave))
fibermap = self._get_fibermap()
frame = Frame(self.wave,
flux,
ivar,
mask,
Rdata,
fibermap=fibermap,
meta=dict(FLAVOR=flavor,
CAMERA=camera,
EXPID=expid,
NIGHT=night,
EXPTIME=1000.))
io.write_frame(self.framefile, frame)
def main_mpi(args, comm=None):
log = get_logger()
psf_file = args.psf
input_file = args.input
# these parameters are interpreted as the *global* spec range,
# to be divided among processes.
specmin = args.specmin
nspec = args.nspec
#- Load input files and broadcast
# FIXME: after we have fixed the serialization
# of the PSF, read and broadcast here, to reduce
# disk contention.
img = None
if comm is None:
img = io.read_image(input_file)
else:
if comm.rank == 0:
img = io.read_image(input_file)
img = comm.bcast(img, root=0)
psf = load_psf(psf_file)
# get spectral range
if nspec is None:
nspec = psf.nspec
specmax = specmin + nspec
camera = img.meta['CAMERA'].lower() #- b0, r1, .. z9
spectrograph = int(camera[1])
fibermin = spectrograph * psf.nspec + specmin
if args.fibermap is not None:
fibermap = io.read_fibermap(args.fibermap)
fibermap = fibermap[fibermin:fibermin + nspec]
fibers = fibermap['FIBER']
else:
fibermap = None
fibers = np.arange(fibermin, fibermin + nspec, dtype='i4')
#- Get wavelength grid from options
if args.wavelength is not None:
wstart, wstop, dw = [float(tmp) for tmp in args.wavelength.split(',')]
else:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.7
wave = np.arange(wstart, wstop + dw / 2.0, dw)
nwave = len(wave)
#- Confirm that this PSF covers these wavelengths for these spectra
psf_wavemin = np.max(psf.wavelength(list(range(specmin, specmax)), y=0))
psf_wavemax = np.min(
psf.wavelength(list(range(specmin, specmax)), y=psf.npix_y - 1))
if psf_wavemin > wstart:
raise ValueError(
'Start wavelength {:.2f} < min wavelength {:.2f} for these fibers'.
format(wstart, psf_wavemin))
if psf_wavemax < wstop:
raise ValueError(
'Stop wavelength {:.2f} > max wavelength {:.2f} for these fibers'.
format(wstop, psf_wavemax))
# Now we divide our spectra into bundles
bundlesize = args.bundlesize
checkbundles = set()
checkbundles.update(
np.floor_divide(np.arange(specmin, specmax),
bundlesize * np.ones(nspec)).astype(int))
bundles = sorted(checkbundles)
nbundle = len(bundles)
bspecmin = {}
bnspec = {}
for b in bundles:
if specmin > b * bundlesize:
bspecmin[b] = specmin
else:
bspecmin[b] = b * bundlesize
if (b + 1) * bundlesize > specmax:
bnspec[b] = specmax - bspecmin[b]
else:
bnspec[b] = bundlesize
# Now we assign bundles to processes
nproc = 1
rank = 0
if comm is not None:
nproc = comm.size
rank = comm.rank
mynbundle = int(nbundle // nproc)
myfirstbundle = 0
leftover = nbundle % nproc
if rank < leftover:
mynbundle += 1
myfirstbundle = rank * mynbundle
else:
myfirstbundle = ((mynbundle + 1) * leftover) + (mynbundle *
(rank - leftover))
if rank == 0:
#- Print parameters
log.info("extract: input = {}".format(input_file))
log.info("extract: psf = {}".format(psf_file))
log.info("extract: specmin = {}".format(specmin))
log.info("extract: nspec = {}".format(nspec))
log.info("extract: wavelength = {},{},{}".format(wstart, wstop, dw))
log.info("extract: nwavestep = {}".format(args.nwavestep))
log.info("extract: regularize = {}".format(args.regularize))
# get the root output file
outpat = re.compile(r'(.*)\.fits')
outmat = outpat.match(args.output)
if outmat is None:
raise RuntimeError(
"extraction output file should have .fits extension")
outroot = outmat.group(1)
outdir = os.path.normpath(os.path.dirname(outroot))
if rank == 0:
if not os.path.isdir(outdir):
os.makedirs(outdir)
if comm is not None:
comm.barrier()
failcount = 0
for b in range(myfirstbundle, myfirstbundle + mynbundle):
outbundle = "{}_{:02d}.fits".format(outroot, b)
outmodel = "{}_model_{:02d}.fits".format(outroot, b)
log.info('extract: Rank {} starting {} spectra {}:{} at {}'.format(
rank,
os.path.basename(input_file),
bspecmin[b],
bspecmin[b] + bnspec[b],
time.asctime(),
))
sys.stdout.flush()
#- The actual extraction
try:
results = ex2d(img.pix,
img.ivar * (img.mask == 0),
psf,
bspecmin[b],
bnspec[b],
wave,
regularize=args.regularize,
ndecorr=args.decorrelate_fibers,
bundlesize=bundlesize,
wavesize=args.nwavestep,
verbose=args.verbose,
full_output=True,
nsubbundles=args.nsubbundles)
flux = results['flux']
ivar = results['ivar']
Rdata = results['resolution_data']
chi2pix = results['chi2pix']
mask = np.zeros(flux.shape, dtype=np.uint32)
mask[results['pixmask_fraction'] > 0.5] |= specmask.SOMEBADPIX
mask[results['pixmask_fraction'] == 1.0] |= specmask.ALLBADPIX
mask[chi2pix > 100.0] |= specmask.BAD2DFIT
#- Augment input image header for output
img.meta['NSPEC'] = (nspec, 'Number of spectra')
img.meta['WAVEMIN'] = (wstart, 'First wavelength [Angstroms]')
img.meta['WAVEMAX'] = (wstop, 'Last wavelength [Angstroms]')
img.meta['WAVESTEP'] = (dw, 'Wavelength step size [Angstroms]')
img.meta['SPECTER'] = (specter.__version__,
'https://github.com/desihub/specter')
img.meta['IN_PSF'] = (_trim(psf_file), 'Input spectral PSF')
img.meta['IN_IMG'] = (_trim(input_file), 'Input image')
if fibermap is not None:
bfibermap = fibermap[bspecmin[b] - specmin:bspecmin[b] +
bnspec[b] - specmin]
else:
bfibermap = None
bfibers = fibers[bspecmin[b] - specmin:bspecmin[b] + bnspec[b] -
specmin]
frame = Frame(wave,
flux,
ivar,
mask=mask,
resolution_data=Rdata,
fibers=bfibers,
meta=img.meta,
fibermap=bfibermap,
chi2pix=chi2pix)
#- Write output
frame.meta['BUNIT'] = 'photon/bin'
io.write_frame(outbundle, frame)
if args.model is not None:
from astropy.io import fits
fits.writeto(outmodel,
results['modelimage'],
header=frame.meta)
log.info('extract: Done {} spectra {}:{} at {}'.format(
os.path.basename(input_file), bspecmin[b],
bspecmin[b] + bnspec[b], time.asctime()))
sys.stdout.flush()
except:
# Log the error and increment the number of failures
log.error(
"extract: FAILED bundle {}, spectrum range {}:{}".format(
b, bspecmin[b], bspecmin[b] + bnspec[b]))
exc_type, exc_value, exc_traceback = sys.exc_info()
lines = traceback.format_exception(exc_type, exc_value,
exc_traceback)
log.error(''.join(lines))
failcount += 1
sys.stdout.flush()
if comm is not None:
failcount = comm.allreduce(failcount)
if failcount > 0:
# all processes throw
raise RuntimeError("some extraction bundles failed")
if rank == 0:
mergeopts = ['--output', args.output, '--force', '--delete']
mergeopts.extend(
["{}_{:02d}.fits".format(outroot, b) for b in bundles])
mergeargs = mergebundles.parse(mergeopts)
mergebundles.main(mergeargs)
if args.model is not None:
model = None
for b in bundles:
outmodel = "{}_model_{:02d}.fits".format(outroot, b)
if model is None:
model = fits.getdata(outmodel)
else:
#- TODO: test and warn if models overlap for pixels with
#- non-zero values
model += fits.getdata(outmodel)
os.remove(outmodel)
fits.writeto(args.model, model)
def main(args):
if args.mpi:
from mpi4py import MPI
comm = MPI.COMM_WORLD
return main_mpi(args, comm)
psf_file = args.psf
input_file = args.input
specmin = args.specmin
nspec = args.nspec
#- Load input files
psf = load_psf(psf_file)
img = io.read_image(input_file)
if nspec is None:
nspec = psf.nspec
specmax = specmin + nspec
camera = img.meta['CAMERA'].lower() #- b0, r1, .. z9
spectrograph = int(camera[1])
fibermin = spectrograph * psf.nspec + specmin
print('Starting {} spectra {}:{} at {}'.format(
os.path.basename(input_file), specmin, specmin + nspec,
time.asctime()))
if args.fibermap is not None:
fibermap = io.read_fibermap(args.fibermap)
fibermap = fibermap[fibermin:fibermin + nspec]
fibers = fibermap['FIBER']
else:
fibermap = None
fibers = np.arange(fibermin, fibermin + nspec, dtype='i4')
#- Get wavelength grid from options
if args.wavelength is not None:
wstart, wstop, dw = [float(tmp) for tmp in args.wavelength.split(',')]
else:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.7
wave = np.arange(wstart, wstop + dw / 2.0, dw)
nwave = len(wave)
bundlesize = args.bundlesize
#- Confirm that this PSF covers these wavelengths for these spectra
psf_wavemin = np.max(psf.wavelength(list(range(specmin, specmax)), y=0))
psf_wavemax = np.min(
psf.wavelength(list(range(specmin, specmax)), y=psf.npix_y - 1))
if psf_wavemin > wstart:
raise ValueError(
'Start wavelength {:.2f} < min wavelength {:.2f} for these fibers'.
format(wstart, psf_wavemin))
if psf_wavemax < wstop:
raise ValueError(
'Stop wavelength {:.2f} > max wavelength {:.2f} for these fibers'.
format(wstop, psf_wavemax))
#- Print parameters
print("""\
#--- Extraction Parameters ---
input: {input}
psf: {psf}
output: {output}
wavelength: {wstart} - {wstop} AA steps {dw}
specmin: {specmin}
nspec: {nspec}
regularize: {regularize}
#-----------------------------\
""".format(input=input_file,
psf=psf_file,
output=args.output,
wstart=wstart,
wstop=wstop,
dw=dw,
specmin=specmin,
nspec=nspec,
regularize=args.regularize))
#- The actual extraction
results = ex2d(img.pix,
img.ivar * (img.mask == 0),
psf,
specmin,
nspec,
wave,
regularize=args.regularize,
ndecorr=args.decorrelate_fibers,
bundlesize=bundlesize,
wavesize=args.nwavestep,
verbose=args.verbose,
full_output=True,
nsubbundles=args.nsubbundles)
flux = results['flux']
ivar = results['ivar']
Rdata = results['resolution_data']
chi2pix = results['chi2pix']
mask = np.zeros(flux.shape, dtype=np.uint32)
mask[results['pixmask_fraction'] > 0.5] |= specmask.SOMEBADPIX
mask[results['pixmask_fraction'] == 1.0] |= specmask.ALLBADPIX
mask[chi2pix > 100.0] |= specmask.BAD2DFIT
#- Augment input image header for output
img.meta['NSPEC'] = (nspec, 'Number of spectra')
img.meta['WAVEMIN'] = (wstart, 'First wavelength [Angstroms]')
img.meta['WAVEMAX'] = (wstop, 'Last wavelength [Angstroms]')
img.meta['WAVESTEP'] = (dw, 'Wavelength step size [Angstroms]')
img.meta['SPECTER'] = (specter.__version__,
'https://github.com/desihub/specter')
img.meta['IN_PSF'] = (_trim(psf_file), 'Input spectral PSF')
img.meta['IN_IMG'] = (_trim(input_file), 'Input image')
frame = Frame(wave,
flux,
ivar,
mask=mask,
resolution_data=Rdata,
fibers=fibers,
meta=img.meta,
fibermap=fibermap,
chi2pix=chi2pix)
#- Write output
frame.meta['BUNIT'] = 'photon/bin'
io.write_frame(args.output, frame)
if args.model is not None:
from astropy.io import fits
fits.writeto(args.model,
results['modelimage'],
header=frame.meta,
clobber=True)
print('Done {} spectra {}:{} at {}'.format(os.path.basename(input_file),
specmin, specmin + nspec,
time.asctime()))
def run_pa(self,
input_image,
psf,
outwave,
boxwidth,
nspec,
fibers=None,
fibermap=None,
dumpfile=None,
maskFile=None,
usesigma=False,
quick_resolution=False):
from lvmspec.boxcar import do_boxcar
from lvmspec.frame import Frame as fr
import lvmspec.psf
if fibermap['OBJTYPE'][0] == 'ARC':
psf = lvmspec.psf.PSF(psf)
flux, ivar, Rdata = do_boxcar(input_image,
psf,
outwave,
boxwidth=boxwidth,
nspec=nspec,
maskFile=maskFile,
usesigma=usesigma,
quick_resolution=quick_resolution)
#- write to a frame object
qndiag = 21
wsigma = None
if quick_resolution:
if hasattr(psf, 'wcoeff'):
wsigma = np.empty(flux.shape)
if isinstance(nspec, (tuple, list, np.ndarray)):
for i, s in enumerate(nspec):
#- GD: Need confirmation, but this appears to be missing.
wsigma[i] = psf.wdisp(
s, outwave) / psf.angstroms_per_pixel(s, outwave)
else:
for i in range(nspec):
wsigma[i] = psf.wdisp(
i, outwave) / psf.angstroms_per_pixel(i, outwave)
elif hasattr(psf, 'xsigma_boot'):
wsigma = np.tile(psf.xsigma_boot, (outwave.shape[0], 1))
frame = fr(outwave,
flux,
ivar,
resolution_data=Rdata,
fibers=fibers,
meta=input_image.meta,
fibermap=fibermap,
wsigma=wsigma,
ndiag=qndiag)
if dumpfile is not None:
from lvmspec import io
night = frame.meta['NIGHT']
expid = frame.meta['EXPID']
io.write_frame(dumpfile, frame)
log.debug("Wrote intermediate file %s after %s" %
(dumpfile, self.name))
return frame