def test_subtract_sky_with_gradient_using_compute_polynomial_times_sky(self):
spectra = self._get_spectra(with_gradient=True)
sky = compute_sky(spectra,angular_variation_deg=1,chromatic_variation_deg=1,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-3, atol=1.)) # this is not exact, it's an iterative fit
def test_subtract_sky_with_gradient_using_compute_non_uniform_sky(self):
spectra = self._get_spectra(with_gradient=True)
sky = compute_sky(spectra,angular_variation_deg=1,chromatic_variation_deg=-1,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-3, atol=1e-3))
def test_subtract_sky_with_gradient_using_compute_non_uniform_sky(self):
spectra = self._get_spectra(with_gradient=True)
sky = compute_sky(spectra,angular_variation_deg=1,chromatic_variation_deg=-1,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-3, atol=1e-3))
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
input_frame=args[0] #- this must be flat field applied before sky subtraction in the pipeline
if "SkyFile" in kwargs:
from desispec.io.sky import read_sky
skyfile=kwargs["SkyFile"] #- Read sky model file itself from an argument
log.info("Using given sky file %s for subtraction"%skyfile)
skymodel=read_sky(skyfile)
else:
if "Outskyfile" in kwargs:
outskyfile=kwargs["Outskyfile"]
else: outskyfile=None
log.info("No sky file given. Computing sky first")
from desispec.quicklook.quicksky import compute_sky
fibermap=input_frame.fibermap
skymodel=compute_sky(input_frame,fibermap)
if outskyfile is not None:
from desispec.io.sky import write_sky
log.info("writing an output sky model file %s "%outskyfile)
write_sky(outputfile,skymodel,input_frame.meta)
#- now do the subtraction
return self.run_pa(input_frame,skymodel)
def test_subtract_sky_with_gradient_using_compute_polynomial_times_sky(self):
spectra = self._get_spectra(with_gradient=True)
sky = compute_sky(spectra,angular_variation_deg=1,chromatic_variation_deg=1,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-3, atol=1e-3)) # this is not exact, it's an iterative fit
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--infile',
type=str,
default=None,
required=True,
help='path of DESI exposure frame fits file')
parser.add_argument('--fibermap',
type=str,
default=None,
required=True,
help='path of DESI exposure frame fits file')
parser.add_argument('--fiberflat',
type=str,
default=None,
required=True,
help='path of DESI fiberflat fits file')
parser.add_argument('--outfile',
type=str,
default=None,
required=True,
help='path of DESI sky fits file')
args = parser.parse_args()
log = get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin = frame.header["SPECMIN"]
specmax = frame.header["SPECMAX"]
# read fibermap to locate sky fibers
fibermap = read_fibermap(args.fibermap)
selection = np.where((fibermap["OBJTYPE"] == "SKY")
& (fibermap["FIBER"] >= specmin)
& (fibermap["FIBER"] <= specmax))[0]
if selection.size == 0:
log.error("no sky fiber in fibermap %s" % args.fibermap)
sys.exit(12)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame, fibermap)
# write result
write_sky(args.outfile, skymodel, frame.header)
log.info("successfully wrote %s" % args.outfile)
def run_pa(self,input_frame,outputfile,fibermap=None): #- input frame should be already fiberflat fielded
from desispec.io.sky import write_sky
from desispec.quicklook.quicksky import compute_sky
skymodel=compute_sky(input_frame,fibermap)
write_sky(outputfile,skymodel,input_frame.meta)
log.info("Sky Model file wrtten. Exiting the pipeline for this configuration")
sys.exit(0)
def run_pa(self,input_frame,outputfile,fibermap=None): #- input frame should be already fiberflat fielded
from desispec.io.sky import write_sky
from desispec.quicklook.quicksky import compute_sky
skymodel=compute_sky(input_frame,fibermap)
write_sky(outputfile,skymodel,input_frame.meta)
log.info("Sky Model file wrtten. Exiting the pipeline for this configuration")
sys.exit(0)
def run_pa(self,input_frame,fiberflat,outputfile):
from desispec.fiberflat import apply_fiberflat
from desispec.sky import compute_sky
from desispec.io.sky import write_sky
#- First apply fiberflat to sky fibers
apply_fiberflat(input_frame,fiberflat)
#- calculate the model
skymodel=compute_sky(input_frame)
write_sky(outputfile,skymodel,input_frame.meta)
log.info("Sky Model file wrtten. Exiting pipeline for this configuration")
sys.exit(0)
def run_pa(self,input_frame,fiberflat,outputfile):
from desispec.fiberflat import apply_fiberflat
from desispec.sky import compute_sky
from desispec.io.sky import write_sky
#- First apply fiberflat to sky fibers
apply_fiberflat(input_frame,fiberflat)
#- calculate the model
skymodel=compute_sky(input_frame)
write_sky(outputfile,skymodel,input_frame.meta)
log.info("Sky Model file wrtten. Exiting pipeline for this configuration")
sys.exit(0)
def main(args) :
log=get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin, specmax = np.min(frame.fibers), np.max(frame.fibers)
if args.cosmics_nsig>0 : # Reject cosmics
reject_cosmic_rays_1d(frame,args.cosmics_nsig)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame,add_variance=(not args.no_extra_variance),\
angular_variation_deg=args.angular_variation_deg,\
chromatic_variation_deg=args.chromatic_variation_deg,\
adjust_wavelength=args.adjust_wavelength,\
adjust_lsf=args.adjust_lsf)
# QA
if (args.qafile is not None) or (args.qafig is not None):
log.info("performing skysub QA")
# Load
qaframe = load_qa_frame(args.qafile, frame_meta=frame.meta, flavor=frame.meta['FLAVOR'])
# Run
qaframe.run_qa('SKYSUB', (frame, skymodel))
# Write
if args.qafile is not None:
write_qa_frame(args.qafile, qaframe)
log.info("successfully wrote {:s}".format(args.qafile))
# Figure(s)
if args.qafig is not None:
qa_plots.frame_skyres(args.qafig, frame, skymodel, qaframe)
# record inputs
frame.meta['IN_FRAME'] = shorten_filename(args.infile)
frame.meta['FIBERFLT'] = shorten_filename(args.fiberflat)
# write result
write_sky(args.outfile, skymodel, frame.meta)
log.info("successfully wrote %s"%args.outfile)
def test_uniform_resolution(self):
#- Setup data for a Resolution matrix
spectra = self._get_spectra()
sky = compute_sky(spectra,add_variance=self.add_variance)
self.assertEqual(sky.flux.shape, spectra.flux.shape)
self.assertEqual(sky.ivar.shape, spectra.ivar.shape)
self.assertEqual(sky.mask.shape, spectra.mask.shape)
delta=spectra.flux[0]-sky.flux[0]
d=np.inner(delta,delta)
self.assertAlmostEqual(d,0.)
delta=spectra.flux[-1]-sky.flux[-1]
d=np.inner(delta,delta)
self.assertAlmostEqual(d,0.)
def test_uniform_resolution(self):
#- Setup data for a Resolution matrix
spectra = self._get_spectra()
sky = compute_sky(spectra,add_variance=self.add_variance)
self.assertEqual(sky.flux.shape, spectra.flux.shape)
self.assertEqual(sky.ivar.shape, spectra.ivar.shape)
self.assertEqual(sky.mask.shape, spectra.mask.shape)
delta=spectra.flux[0]-sky.flux[0]
d=np.inner(delta,delta)
self.assertAlmostEqual(d,0.)
delta=spectra.flux[-1]-sky.flux[-1]
d=np.inner(delta,delta)
self.assertAlmostEqual(d,0.)
def main() :
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--infile', type = str, default = None, required=True,
help = 'path of DESI exposure frame fits file')
parser.add_argument('--fibermap', type = str, default = None, required=True,
help = 'path of DESI exposure frame fits file')
parser.add_argument('--fiberflat', type = str, default = None, required=True,
help = 'path of DESI fiberflat fits file')
parser.add_argument('--outfile', type = str, default = None, required=True,
help = 'path of DESI sky fits file')
args = parser.parse_args()
log=get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin=frame.header["SPECMIN"]
specmax=frame.header["SPECMAX"]
# read fibermap to locate sky fibers
fibermap = read_fibermap(args.fibermap)
selection=np.where((fibermap["OBJTYPE"]=="SKY")&(fibermap["FIBER"]>=specmin)&(fibermap["FIBER"]<=specmax))[0]
if selection.size == 0 :
log.error("no sky fiber in fibermap %s"%args.fibermap)
sys.exit(12)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame, fibermap)
# write result
write_sky(args.outfile, skymodel, frame.header)
log.info("successfully wrote %s"%args.outfile)
def run_pa(self,
input_frame,
outputfile,
fibermap=None,
apply_resolution=False
): #- input frame should be already fiberflat fielded
from desispec.io.sky import write_sky
from desispec.quicklook.quicksky import compute_sky
skymodel = compute_sky(input_frame,
fibermap,
apply_resolution=apply_resolution)
write_sky(outputfile, skymodel, input_frame.meta)
# SEE ABOVE COMMENT!!!!
log.debug(
"Sky Model file wrtten. Exiting the pipeline for this configuration"
)
sys.exit(0)
def main(args):
log = get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin, specmax = np.min(frame.fibers), np.max(frame.fibers)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame)
# QA
if (args.qafile is not None) or (args.qafig is not None):
log.info("performing skysub QA")
# Load
qaframe = load_qa_frame(args.qafile,
frame,
flavor=frame.meta['FLAVOR'])
# Run
qaframe.run_qa('SKYSUB', (frame, skymodel))
# Write
if args.qafile is not None:
write_qa_frame(args.qafile, qaframe)
log.info("successfully wrote {:s}".format(args.qafile))
# Figure(s)
if args.qafig is not None:
qa_plots.frame_skyres(args.qafig, frame, skymodel, qaframe)
# write result
write_sky(args.outfile, skymodel, frame.meta)
log.info("successfully wrote %s" % args.outfile)
def main(args) :
log=get_logger()
log.info("starting")
# read exposure to load data and get range of spectra
frame = read_frame(args.infile)
specmin, specmax = np.min(frame.fibers), np.max(frame.fibers)
# read fiberflat
fiberflat = read_fiberflat(args.fiberflat)
# apply fiberflat to sky fibers
apply_fiberflat(frame, fiberflat)
# compute sky model
skymodel = compute_sky(frame)
# QA
if (args.qafile is not None) or (args.qafig is not None):
log.info("performing skysub QA")
# Load
qaframe = load_qa_frame(args.qafile, frame, flavor=frame.meta['FLAVOR'])
# Run
qaframe.run_qa('SKYSUB', (frame, skymodel))
# Write
if args.qafile is not None:
write_qa_frame(args.qafile, qaframe)
log.info("successfully wrote {:s}".format(args.qafile))
# Figure(s)
if args.qafig is not None:
qa_plots.frame_skyres(args.qafig, frame, skymodel, qaframe)
# write result
write_sky(args.outfile, skymodel, frame.meta)
log.info("successfully wrote %s"%args.outfile)
def test_subtract_sky(self):
spectra = self._get_spectra()
sky = compute_sky(spectra,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-5, atol=1e-6))
def test_subtract_sky(self):
spectra = self._get_spectra()
sky = compute_sky(spectra,add_variance=self.add_variance)
subtract_sky(spectra, sky)
#- allow some slop in the sky subtraction
self.assertTrue(np.allclose(spectra.flux, 0, rtol=1e-5, atol=1e-6))
