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('--fiberflat', type = str, default = None, help = 'path of DESI fiberflat fits file') parser.add_argument('--sky', type = str, default = None, help = 'path of DESI sky fits file') parser.add_argument('--calib', type = str, default = None, help = 'path of DESI calibration fits file') parser.add_argument('--outfile', type = str, default = None, required=True, help = 'path of DESI sky fits file') # add calibration here when exists args = parser.parse_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.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) # save output write_frame(args.outfile, frame) log.info("successfully wrote %s"%args.outfile)
def test_apply_fluxcalibration(self): #get frame_data wave = np.arange(5000, 6000) nwave = len(wave) nspec = 3 flux = np.random.uniform(0.9, 1.0, size=(nspec, nwave)) ivar = np.ones_like(flux) origframe = Frame(wave, flux, ivar, spectrograph=0) #define fluxcalib object calib = np.ones_like(origframe.flux) mask = np.zeros(origframe.flux.shape, dtype=np.uint32) calib[0] *= 0.5 calib[1] *= 1.5 # fc with essentially no error fcivar = 1e20 * np.ones_like(origframe.flux) fc = FluxCalib(origframe.wave, calib, fcivar,mask) frame = copy.deepcopy(origframe) apply_flux_calibration(frame, fc) self.assertTrue(np.allclose(frame.ivar, calib**2)) # origframe.flux=0 should result in frame.flux=0 fcivar = np.ones_like(origframe.flux) calib = np.ones_like(origframe.flux) fc = FluxCalib(origframe.wave, calib, fcivar, mask) frame = copy.deepcopy(origframe) frame.flux[0,0:10]=0.0 apply_flux_calibration(frame, fc) self.assertTrue(np.all(frame.flux[0, 0:10] == 0.0)) #fcivar=0 should result in frame.ivar=0 fcivar=np.ones_like(origframe.flux) calib=np.ones_like(origframe.flux) fcivar[0,0:10]=0.0 fc=FluxCalib(origframe.wave,calib,fcivar,mask) frame=copy.deepcopy(origframe) apply_flux_calibration(frame,fc) self.assertTrue(np.all(frame.ivar[0,0:10]==0.0)) # should also work even the calib =0 ?? #fcivar=np.ones_like(origframe.flux) #calib=np.ones_like(origframe.flux) #fcivar[0,0:10]=0.0 #calib[0,0:10]=0.0 #fc=FluxCalib(origframe.wave,calib,fcivar,mask) #frame=copy.deepcopy(origframe) #apply_flux_calibration(frame,fc) #self.assertTrue(np.all(frame.ivar[0,0:10]==0.0)) # test different wavelength bins frame=copy.deepcopy(origframe) calib = np.ones_like(frame.flux) fcivar=np.ones_like(frame.ivar) mask=np.zeros(origframe.flux.shape, dtype=np.uint32) fc=FluxCalib(origframe.wave+0.01,calib,fcivar,mask) with self.assertRaises(SystemExit): #should be ValueError instead? apply_flux_calibration(frame,fc)
def test_apply_fluxcalibration(self): #get frame_data wave = np.arange(5000, 6000) nwave = len(wave) nspec = 3 flux = np.random.uniform(0.9, 1.0, size=(nspec, nwave)) ivar = np.ones_like(flux) origframe = Frame(wave, flux, ivar, spectrograph=0) #define fluxcalib object calib = np.ones_like(origframe.flux) mask = np.zeros(origframe.flux.shape, dtype=np.uint32) calib[0] *= 0.5 calib[1] *= 1.5 # fc with essentially no error fcivar = 1e20 * np.ones_like(origframe.flux) fc = FluxCalib(origframe.wave, calib, fcivar,mask) frame = copy.deepcopy(origframe) apply_flux_calibration(frame, fc) self.assertTrue(np.allclose(frame.ivar, calib**2)) # origframe.flux=0 should result in frame.flux=0 fcivar = np.ones_like(origframe.flux) calib = np.ones_like(origframe.flux) fc = FluxCalib(origframe.wave, calib, fcivar, mask) frame = copy.deepcopy(origframe) frame.flux[0,0:10]=0.0 apply_flux_calibration(frame, fc) self.assertTrue(np.all(frame.flux[0, 0:10] == 0.0)) #fcivar=0 should result in frame.ivar=0 fcivar=np.ones_like(origframe.flux) calib=np.ones_like(origframe.flux) fcivar[0,0:10]=0.0 fc=FluxCalib(origframe.wave,calib,fcivar,mask) frame=copy.deepcopy(origframe) apply_flux_calibration(frame,fc) self.assertTrue(np.all(frame.ivar[0,0:10]==0.0)) # should also work even the calib =0 ?? #fcivar=np.ones_like(origframe.flux) #calib=np.ones_like(origframe.flux) #fcivar[0,0:10]=0.0 #calib[0,0:10]=0.0 #fc=FluxCalib(origframe.wave,calib,fcivar,mask) #frame=copy.deepcopy(origframe) #apply_flux_calibration(frame,fc) #self.assertTrue(np.all(frame.ivar[0,0:10]==0.0)) # test different wavelength bins frame=copy.deepcopy(origframe) calib = np.ones_like(frame.flux) fcivar=np.ones_like(frame.ivar) mask=np.zeros(origframe.flux.shape, dtype=np.uint32) fc=FluxCalib(origframe.wave+0.01,calib,fcivar,mask) with self.assertRaises(SystemExit): #should be ValueError instead? apply_flux_calibration(frame,fc)
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.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) # save output write_frame(args.outfile, frame, units='1e-17 erg/(s cm2 A)') log.info("successfully wrote %s"%args.outfile)
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('--fiberflat', type=str, default=None, help='path of DESI fiberflat fits file') parser.add_argument('--sky', type=str, default=None, help='path of DESI sky fits file') parser.add_argument('--calib', type=str, default=None, help='path of DESI calibration fits file') parser.add_argument('--outfile', type=str, default=None, required=True, help='path of DESI sky fits file') # add calibration here when exists args = parser.parse_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.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) # save output write_frame(args.outfile, frame) log.info("successfully wrote %s" % args.outfile)
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) #- Raw scores already added in extraction, but just in case they weren't #- it is harmless to rerun to make sure we have them. compute_and_append_frame_scores(frame, suffix="RAW") if args.cosmics_nsig > 0 and args.sky == None: # Reject cosmics (otherwise do it after sky subtraction) log.info("cosmics ray 1D rejection") 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 all fibers apply_fiberflat(frame, fiberflat) compute_and_append_frame_scores(frame, suffix="FFLAT") if args.sky != None: # read sky skymodel = read_sky(args.sky) if args.cosmics_nsig > 0: # first subtract sky without throughput correction subtract_sky(frame, skymodel, throughput_correction=False) # then find cosmics log.info("cosmics ray 1D rejection after sky subtraction") reject_cosmic_rays_1d(frame, args.cosmics_nsig) if args.sky_throughput_correction: # and (re-)subtract sky, but just the correction term subtract_sky(frame, skymodel, throughput_correction=True, default_throughput_correction=0.) else: # subtract sky subtract_sky(frame, skymodel, throughput_correction=args.sky_throughput_correction) compute_and_append_frame_scores(frame, suffix="SKYSUB") if args.calib != None: log.info("calibrate") # read calibration fluxcalib = read_flux_calibration(args.calib) # apply calibration apply_flux_calibration(frame, fluxcalib) compute_and_append_frame_scores(frame, suffix="CALIB") # save output write_frame(args.outfile, frame, units='1e-17 erg/(s cm2 Angstrom)') log.info("successfully wrote %s" % args.outfile)
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) #- Raw scores already added in extraction, but just in case they weren't #- it is harmless to rerun to make sure we have them. compute_and_append_frame_scores(frame,suffix="RAW") if args.cosmics_nsig>0 and args.sky==None : # Reject cosmics (otherwise do it after sky subtraction) log.info("cosmics ray 1D rejection") 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 all fibers apply_fiberflat(frame, fiberflat) compute_and_append_frame_scores(frame,suffix="FFLAT") if args.sky!=None : # read sky skymodel=read_sky(args.sky) if args.cosmics_nsig>0 : # use a copy the frame (not elegant but robust) copied_frame = copy.deepcopy(frame) # first subtract sky without throughput correction subtract_sky(copied_frame, skymodel, apply_throughput_correction = False) # then find cosmics log.info("cosmics ray 1D rejection after sky subtraction") reject_cosmic_rays_1d(copied_frame,args.cosmics_nsig) # copy mask frame.mask = copied_frame.mask # and (re-)subtract sky, but just the correction term subtract_sky(frame, skymodel, apply_throughput_correction = (not args.no_sky_throughput_correction) ) else : # subtract sky subtract_sky(frame, skymodel, apply_throughput_correction = (not args.no_sky_throughput_correction) ) compute_and_append_frame_scores(frame,suffix="SKYSUB") if args.calib!=None : log.info("calibrate") # read calibration fluxcalib=read_flux_calibration(args.calib) # apply calibration apply_flux_calibration(frame, fluxcalib) # Ensure that ivars are set to 0 for all values if any designated # fibermask bit is set. Also flips a bits for each frame.mask value using specmask.BADFIBER frame = get_fiberbitmasked_frame(frame,bitmask="flux",ivar_framemask=True) compute_and_append_frame_scores(frame,suffix="CALIB") # save output write_frame(args.outfile, frame, units='10**-17 erg/(s cm2 Angstrom)') log.info("successfully wrote %s"%args.outfile)
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) if (not args.no_tsnr) and (args.calib is None): log.critical( 'need --fiberflat --sky and --calib to compute template SNR') sys.exit(12) frame = read_frame(args.infile) if not args.no_tsnr: # tsnr alpha calc. requires uncalibrated + no substraction rame. uncalibrated_frame = copy.deepcopy(frame) #- Raw scores already added in extraction, but just in case they weren't #- it is harmless to rerun to make sure we have them. compute_and_append_frame_scores(frame, suffix="RAW") if args.cosmics_nsig > 0 and args.sky == None: # Reject cosmics (otherwise do it after sky subtraction) log.info("cosmics ray 1D rejection") 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 all fibers apply_fiberflat(frame, fiberflat) compute_and_append_frame_scores(frame, suffix="FFLAT") else: fiberflat = None if args.no_xtalk: zero_ivar = (not args.no_zero_ivar) else: zero_ivar = False if args.sky != None: # read sky skymodel = read_sky(args.sky) if args.cosmics_nsig > 0: # use a copy the frame (not elegant but robust) copied_frame = copy.deepcopy(frame) # first subtract sky without throughput correction subtract_sky(copied_frame, skymodel, apply_throughput_correction=False, zero_ivar=zero_ivar) # then find cosmics log.info("cosmics ray 1D rejection after sky subtraction") reject_cosmic_rays_1d(copied_frame, args.cosmics_nsig) # copy mask frame.mask = copied_frame.mask # and (re-)subtract sky, but just the correction term subtract_sky(frame, skymodel, apply_throughput_correction=( not args.no_sky_throughput_correction), zero_ivar=zero_ivar) else: # subtract sky subtract_sky(frame, skymodel, apply_throughput_correction=( not args.no_sky_throughput_correction), zero_ivar=zero_ivar) compute_and_append_frame_scores(frame, suffix="SKYSUB") if not args.no_xtalk: log.info("fiber crosstalk correction") correct_fiber_crosstalk(frame, fiberflat) if not args.no_zero_ivar: frame.ivar *= (frame.mask == 0) if args.calib != None: log.info("calibrate") # read calibration fluxcalib = read_flux_calibration(args.calib) # apply calibration apply_flux_calibration(frame, fluxcalib) # Ensure that ivars are set to 0 for all values if any designated # fibermask bit is set. Also flips a bits for each frame.mask value using specmask.BADFIBER frame = get_fiberbitmasked_frame( frame, bitmask="flux", ivar_framemask=(not args.no_zero_ivar)) compute_and_append_frame_scores(frame, suffix="CALIB") if not args.no_tsnr: log.info("calculating tsnr") results, alpha = calc_tsnr2(uncalibrated_frame, fiberflat=fiberflat, skymodel=skymodel, fluxcalib=fluxcalib, alpha_only=args.alpha_only) frame.meta['TSNRALPH'] = alpha comments = {k: "from calc_frame_tsnr" for k in results.keys()} append_frame_scores(frame, results, comments, overwrite=True) # record inputs frame.meta['IN_FRAME'] = shorten_filename(args.infile) frame.meta['FIBERFLT'] = shorten_filename(args.fiberflat) frame.meta['IN_SKY'] = shorten_filename(args.sky) frame.meta['IN_CALIB'] = shorten_filename(args.calib) # save output write_frame(args.outfile, frame, units='10**-17 erg/(s cm2 Angstrom)') log.info("successfully wrote %s" % args.outfile)