def main_mpi(args, comm=None):
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 = map(float, args.wavelength.split(','))
else:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.5
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(range(specmin, specmax), y=0))
psf_wavemax = np.min(psf.wavelength(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(list(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
print "extract: input = {}".format(input_file)
print "extract: psf = {}".format(psf_file)
print "extract: specmin = {}".format(specmin)
print "extract: nspec = {}".format(nspec)
print "extract: wavelength = {},{},{}".format(wstart, wstop, dw)
print "extract: nwavestep = {}".format(args.nwavestep)
print "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)
print('extract: Rank {} starting {} spectra {}:{} at {}'.format(
rank, os.path.basename(input_file),
bspecmin[b], bspecmin[b]+bnspec[b], time.asctime(),
) )
#- The actual extraction
try:
results = ex2d(img.pix, img.ivar*(img.mask==0), psf, bspecmin[b],
bnspec[b], wave, regularize=args.regularize, ndecorr=True,
bundlesize=bundlesize, wavesize=args.nwavestep, verbose=args.verbose,
full_output=True)
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
io.write_frame(outbundle, frame)
if args.model is not None:
from astropy.io import fits
fits.writeto(outmodel, results['modelimage'], header=frame.meta)
print('extract: Done {} spectra {}:{} at {}'.format(os.path.basename(input_file),
bspecmin[b], bspecmin[b]+bnspec[b], time.asctime()))
except:
failcount += 1
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_mpi(args, comm=None, timing=None):
freeze_iers()
nproc = 1
rank = 0
if comm is not None:
nproc = comm.size
rank = comm.rank
mark_start = time.time()
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 rank == 0:
img = io.read_image(input_file)
if comm is not None:
img = comm.bcast(img, root=0)
psf = load_psf(psf_file)
mark_read_input = time.time()
# get spectral range
if nspec is None:
nspec = psf.nspec
if args.fibermap is not None:
fibermap = io.read_fibermap(args.fibermap)
else:
try:
fibermap = io.read_fibermap(args.input)
except (AttributeError, IOError, KeyError):
fibermap = None
if fibermap is not None:
fibermap = fibermap[specmin:specmin + nspec]
if nspec > len(fibermap):
log.warning(
"nspec {} > len(fibermap) {}; reducing nspec to {}".format(
nspec, len(fibermap), len(fibermap)))
nspec = len(fibermap)
fibers = fibermap['FIBER']
else:
fibers = np.arange(specmin, specmin + nspec)
specmax = specmin + nspec
#- Get wavelength grid from options
if args.wavelength is not None:
raw_wstart, raw_wstop, raw_dw = [
float(tmp) for tmp in args.wavelength.split(',')
]
else:
raw_wstart = np.ceil(psf.wmin_all)
raw_wstop = np.floor(psf.wmax_all)
raw_dw = 0.7
raw_wave = np.arange(raw_wstart, raw_wstop + raw_dw / 2.0, raw_dw)
nwave = len(raw_wave)
bundlesize = args.bundlesize
if args.barycentric_correction:
if ('RA' in img.meta) or ('TARGTRA' in img.meta):
barycentric_correction_factor = \
barycentric_correction_multiplicative_factor(img.meta)
#- Early commissioning has RA/TARGTRA in fibermap but not HDU 0
elif fibermap is not None and \
(('RA' in fibermap.meta) or ('TARGTRA' in fibermap.meta)):
barycentric_correction_factor = \
barycentric_correction_multiplicative_factor(fibermap.meta)
else:
msg = 'Barycentric corr requires (TARGT)RA in HDU 0 or fibermap'
log.critical(msg)
raise KeyError(msg)
else:
barycentric_correction_factor = 1.
# Explictly define the correct wavelength values to avoid confusion of reference frame
# If correction applied, otherwise divide by 1 and use the same raw values
wstart = raw_wstart / barycentric_correction_factor
wstop = raw_wstop / barycentric_correction_factor
dw = raw_dw / barycentric_correction_factor
wave = raw_wave / barycentric_correction_factor
#- Confirm that this PSF covers these wavelengths for these spectra
psf_wavemin = np.max(psf.wavelength(list(range(specmin, specmax)), y=-0.5))
psf_wavemax = np.min(
psf.wavelength(list(range(specmin, specmax)), y=psf.npix_y - 0.5))
if psf_wavemin - 5 > wstart:
raise ValueError(
'Start wavelength {:.2f} < min wavelength {:.2f} for these fibers'.
format(wstart, psf_wavemin))
if psf_wavemax + 5 < wstop:
raise ValueError(
'Stop wavelength {:.2f} > max wavelength {:.2f} for these fibers'.
format(wstop, psf_wavemax))
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))
if barycentric_correction_factor != 1.:
img.meta['HELIOCOR'] = barycentric_correction_factor
#- Augment input image header for output
img.meta['NSPEC'] = (nspec, 'Number of spectra')
img.meta['WAVEMIN'] = (raw_wstart, 'First wavelength [Angstroms]')
img.meta['WAVEMAX'] = (raw_wstop, 'Last wavelength [Angstroms]')
img.meta['WAVESTEP'] = (raw_dw, 'Wavelength step size [Angstroms]')
img.meta['SPECTER'] = (specter.__version__,
'https://github.com/desihub/specter')
img.meta['IN_PSF'] = (io.shorten_filename(psf_file), 'Input spectral PSF')
img.meta['IN_IMG'] = io.shorten_filename(input_file)
depend.add_dependencies(img.meta)
#- Check if input PSF was itself a traceshifted version of another PSF
orig_psf = None
if rank == 0:
try:
psfhdr = fits.getheader(psf_file, 'PSF')
orig_psf = psfhdr['IN_PSF']
except KeyError:
#- could happen due to PSF format not having "PSF" extension,
#- or due to PSF header not having 'IN_PSF' keyword. Either is OK
pass
if comm is not None:
orig_psf = comm.bcast(orig_psf, root=0)
if orig_psf is not None:
img.meta['ORIG_PSF'] = orig_psf
#- If not using MPI, use a single call to each of these and then end this function call
# Otherwise, continue on to splitting things up for the different ranks
if comm is None:
_extract_and_save(img, psf, specmin, nspec, specmin, wave, raw_wave,
fibers, fibermap, args.output, args.model,
bundlesize, args, log)
#- This is it if we aren't running MPI, so return
return
#else:
# # Continue to the MPI section, which could go under this else statment
# # But to save on indentation we'll just pass on to the rest of the function
# # since the alternative has already returned
# pass
# Now we divide our spectra into bundles
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
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))
# 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()
mark_preparation = time.time()
time_total_extraction = 0.0
time_total_write_output = 0.0
failcount = 0
for b in range(myfirstbundle, myfirstbundle + mynbundle):
mark_iteration_start = time.time()
outbundle = "{}_{:02d}.fits".format(outroot, b)
outmodel = "{}_model_{:02d}.fits".format(outroot, b)
log.info('extract: Rank {} extracting {} spectra {}:{} at {}'.format(
rank,
os.path.basename(input_file),
bspecmin[b],
bspecmin[b] + bnspec[b],
time.asctime(),
))
sys.stdout.flush()
#- The actual extraction
try:
mark_extraction = _extract_and_save(img, psf, bspecmin[b],
bnspec[b], specmin, wave,
raw_wave, fibers, fibermap,
outbundle, outmodel,
bundlesize, args, log)
mark_write_output = time.time()
time_total_extraction += mark_extraction - mark_iteration_start
time_total_write_output += mark_write_output - mark_extraction
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")
time_merge = None
if rank == 0:
mark_merge_start = time.time()
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)
mark_merge_end = time.time()
time_merge = mark_merge_end - mark_merge_start
# Resolve difference timer data
if type(timing) is dict:
timing["read_input"] = mark_read_input - mark_start
timing["preparation"] = mark_preparation - mark_read_input
timing["total_extraction"] = time_total_extraction
timing["total_write_output"] = time_total_write_output
timing["merge"] = time_merge
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 = 0.5
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=True,
bundlesize=bundlesize,
wavesize=args.nwavestep,
verbose=args.verbose,
full_output=True)
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
io.write_frame(outbundle, frame, units='photon/bin')
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_mpi(args, comm=None):
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 = map(float, args.wavelength.split(','))
else:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.5
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(range(specmin, specmax), y=0))
psf_wavemax = np.min(
psf.wavelength(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(list(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
print "extract: input = {}".format(input_file)
print "extract: psf = {}".format(psf_file)
print "extract: specmin = {}".format(specmin)
print "extract: nspec = {}".format(nspec)
print "extract: wavelength = {},{},{}".format(wstart, wstop, dw)
print "extract: nwavestep = {}".format(args.nwavestep)
print "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.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)
print('extract: Starting {} spectra {}:{} at {}'.format(
os.path.basename(input_file), bspecmin[b], bspecmin[b] + bnspec[b],
time.asctime()))
#- The actual extraction
try:
flux, ivar, Rdata = ex2d(img.pix,
img.ivar * (img.mask == 0),
psf,
bspecmin[b],
bnspec[b],
wave,
regularize=args.regularize,
ndecorr=True,
bundlesize=bundlesize,
wavesize=args.nwavestep,
verbose=args.verbose)
#- 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')
bfibermap = fibermap[bspecmin[b] - specmin:bspecmin[b] +
bnspec[b] - specmin]
bfibers = fibers[bspecmin[b] - specmin:bspecmin[b] + bnspec[b] -
specmin]
frame = Frame(wave,
flux,
ivar,
resolution_data=Rdata,
fibers=bfibers,
meta=img.meta,
fibermap=bfibermap)
#- Write output
io.write_frame(outbundle, frame)
print('extract: Done {} spectra {}:{} at {}'.format(
os.path.basename(input_file), bspecmin[b],
bspecmin[b] + bnspec[b], time.asctime()))
except:
failcount += 1
if comm is not None:
failcount = comm.allreduce(failcount)
if failcount > 0:
# all processes throw
raise RuntimeError("some extraction bundles failed")
if rank == 0:
opts = ['--output', args.output, '--force', '--delete']
opts.extend(["{}_{:02d}.fits".format(outroot, b) for b in bundles])
args = merge.parse(opts)
merge.main(args)