def test_wavelengths(self): if self.data_unavailable: self.skipTest("Failed to download test data.") # Read flat flat_hdu = fits.open(self.testflat) header = flat_hdu[0].header flat = flat_hdu[0].data ny = flat.shape[0] # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat, xpk, ypos) xfit, fdicts = desiboot.fit_traces(xset, xerr) # Test fiber_gauss_old for coverage gauss = desiboot.fiber_gauss_old(flat, xfit, xerr) # Gaussian gauss = desiboot.fiber_gauss(flat, xfit, xerr) # Read arc arc_hdu = fits.open(self.testarc) arc = arc_hdu[0].data arc_ivar = np.ones(arc.shape) # Extract arc spectra (one per fiber) all_spec = desiboot.extract_sngfibers_gaussianpsf(arc, arc_ivar, xfit, gauss) # Line list camera = header['CAMERA'] llist = desiboot.load_arcline_list(camera) dlamb, gd_lines = desiboot.load_gdarc_lines(camera,llist) # all_wv_soln = [] for ii in range(1): spec = all_spec[:,ii] # Find Lines pixpk, flux = desiboot.find_arc_lines(spec) id_dict = {"pixpk":pixpk,"flux":flux} # Match a set of 5 gd_lines to detected lines desiboot.id_arc_lines_using_triplets(id_dict,gd_lines,dlamb) # Now the rest desiboot.id_remainder(id_dict, llist, deg=3) # Final fit wave vs. pix too final_fit, mask = dufits.iter_fit(np.array(id_dict['id_wave']), np.array(id_dict['id_pix']), 'polynomial', 3, xmin=0., xmax=1.) rms = np.sqrt(np.mean((dufits.func_val( np.array(id_dict['id_wave'])[mask==0], final_fit)- np.array(id_dict['id_pix'])[mask==0])**2)) final_fit_pix,mask2 = dufits.iter_fit(np.array(id_dict['id_pix']), np.array(id_dict['id_wave']), 'legendre',4, niter=5) # Save id_dict['final_fit'] = final_fit id_dict['rms'] = rms id_dict['final_fit_pix'] = final_fit_pix id_dict['wave_min'] = dufits.func_val(0, final_fit_pix) id_dict['wave_max'] = dufits.func_val(ny-1, final_fit_pix) id_dict['mask'] = mask all_wv_soln.append(id_dict) self.assertLess(all_wv_soln[0]['rms'], 0.25)
def test_tracing(self): if self.data_unavailable: self.skipTest("Failed to download test data.") flat_hdu = fits.open(self.testflat) flat = flat_hdu[0].data # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat,xpk,ypos) xfit, fdicts = desiboot.fit_traces(xset,xerr)
def test_tracing(self): if self.data_unavailable: self.skipTest("Failed to download test data.") flat_hdu = fits.open(self.testflat) flat = flat_hdu[0].data # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat, xpk, ypos) xfit, fdicts = desiboot.fit_traces(xset, xerr)
def test_gauss(self): if self.data_unavailable: self.skipTest("Failed to download test data.") flat_hdu = fits.open(self.testflat) flat = flat_hdu[0].data # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat, xpk, ypos) xfit, fdicts = desiboot.fit_traces(xset, xerr) # Gaussian gauss = desiboot.fiber_gauss(flat, xfit, xerr) #import pdb #pdb.set_trace() np.testing.assert_allclose(np.median(gauss), 1.06, rtol=0.05)
def test_gauss(self): if self.data_unavailable: self.skipTest("Failed to download test data.") flat_hdu = fits.open(self.testflat) flat = flat_hdu[0].data # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat, xpk, ypos) xfit, fdicts = desiboot.fit_traces(xset, xerr) # Gaussian gauss = desiboot.fiber_gauss(flat, xfit, xerr) #import pdb #pdb.set_trace() np.testing.assert_allclose(np.median(gauss), 1.06, rtol=0.05)
def test_wavelengths(self): if self.data_unavailable: self.skipTest("Failed to download test data.") # Read flat flat_hdu = fits.open(self.testflat) header = flat_hdu[0].header flat = flat_hdu[0].data ny = flat.shape[0] # Find fibers (necessary) xpk, ypos, cut = desiboot.find_fiber_peaks(flat) # Trace xset, xerr = desiboot.trace_crude_init(flat, xpk, ypos) xfit, fdicts = desiboot.fit_traces(xset, xerr) # Test fiber_gauss_old for coverage gauss = desiboot.fiber_gauss_old(flat, xfit, xerr) # Gaussian gauss = desiboot.fiber_gauss(flat, xfit, xerr) # Read arc arc_hdu = fits.open(self.testarc) arc = arc_hdu[0].data arc_ivar = np.ones(arc.shape) # Extract arc spectra (one per fiber) all_spec = desiboot.extract_sngfibers_gaussianpsf( arc, arc_ivar, xfit, gauss) # Line list camera = header['CAMERA'] llist = desiboot.load_arcline_list(camera) dlamb, gd_lines = desiboot.load_gdarc_lines(camera, llist) # all_wv_soln = [] for ii in range(1): spec = all_spec[:, ii] # Find Lines pixpk, flux = desiboot.find_arc_lines(spec) id_dict = {"pixpk": pixpk, "flux": flux} # Match a set of 5 gd_lines to detected lines desiboot.id_arc_lines_using_triplets(id_dict, gd_lines, dlamb) # Now the rest desiboot.id_remainder(id_dict, llist, deg=3) # Final fit wave vs. pix too final_fit, mask = dufits.iter_fit(np.array(id_dict['id_wave']), np.array(id_dict['id_pix']), 'polynomial', 3, xmin=0., xmax=1.) rms = np.sqrt( np.mean((dufits.func_val( np.array(id_dict['id_wave'])[mask == 0], final_fit) - np.array(id_dict['id_pix'])[mask == 0])**2)) final_fit_pix, mask2 = dufits.iter_fit(np.array(id_dict['id_pix']), np.array( id_dict['id_wave']), 'legendre', 4, niter=5) # Save id_dict['final_fit'] = final_fit id_dict['rms'] = rms id_dict['final_fit_pix'] = final_fit_pix id_dict['wave_min'] = dufits.func_val(0, final_fit_pix) id_dict['wave_max'] = dufits.func_val(ny - 1, final_fit_pix) id_dict['mask'] = mask all_wv_soln.append(id_dict) self.assertLess(all_wv_soln[0]['rms'], 0.25)
def main(args): log=get_logger() log.info("Starting") if args.triplet_matching : log.warning("triplet_matching option deprecated, this algorithm is now used for all cases") lamps=None if args.lamps : lamps=np.array(args.lamps.split(",")) log.info("Using lamps = %s"%str(lamps)) else : log.info("Using default set of lamps") if args.fiberflat is not None and args.contfile is None : args.contfile=args.fiberflat log.warning("Please use --contfile instead of --fiberflat") if (args.psffile is None) and (args.contfile is None): raise IOError("Must provide either a PSF file or a contfile") # Start QA try: pp = PdfPages(args.qafile) except ValueError: QA = False else: QA = True contfile_header = None if args.psffile is None: ########### # Read continuum cont_hdu = fits.open(args.contfile) contfile_header = cont_hdu[0].header header = cont_hdu[0].header if len(cont_hdu)>=3 : cont = cont_hdu[0].data*(cont_hdu[1].data>0)*(cont_hdu[2].data==0) else : cont = cont_hdu[0].data log.warning("found only %d HDU in cont, do not use ivar"%len(cont_hdu)) ny = cont.shape[0] ########### # Find fibers log.info("Finding the fibers") xpk, ypos, cut = desiboot.find_fiber_peaks(cont) if QA: desiboot.qa_fiber_peaks(xpk, cut, pp) # Test? if args.test: log.warning("cutting down fibers for testing..") #xpk = xpk[0:100] xpk = xpk[0:50] #xpk = xpk[0:5] ########### # Trace the fiber cont spectra log.info("Tracing the continuum spectra") # Crude first log.info("Crudely..") xset, xerr = desiboot.trace_crude_init(cont,xpk,ypos) # Polynomial fits log.info("Fitting the traces") xfit, fdicts = desiboot.fit_traces(xset,xerr) # QA if QA: desiboot.qa_fiber_Dx(xfit, fdicts, pp) ########### # Model the PSF with Gaussian log.info("Modeling the PSF with a Gaussian, be patient..") gauss = desiboot.fiber_gauss(cont,xfit,xerr) if QA: desiboot.qa_fiber_gauss(gauss, pp) XCOEFF = None else: # Load PSF file and generate trace info log.warning("Not tracing the continuum. Using the PSF file.") psf_hdu = fits.open(args.psffile) psf_head = psf_hdu[0].header # Gaussians gauss = psf_hdu[2].data # Traces WAVEMIN = psf_head['WAVEMIN'] WAVEMAX = psf_head['WAVEMAX'] XCOEFF = psf_hdu[0].data xfit = None fdicts = None arc_header = None # ARCS if not args.trace_only: ########### # Read arc log.info("Reading arc") arc_hdu = fits.open(args.arcfile) arc_header = arc_hdu[0].header if len(arc_hdu)>=3 : # set to zero ivar of masked pixels, force positive or null ivar arc_ivar = arc_hdu[1].data*(arc_hdu[2].data==0)*(arc_hdu[1].data>0) # and mask pixels below -5 sigma (cures unmasked dead columns in sims.) arc_ivar *= (arc_hdu[0].data*np.sqrt(arc_hdu[1].data)>-5.) # set to zero pixel values with null ivar arc = arc_hdu[0].data*(arc_ivar>0) else : arc = arc_hdu[0].data arc_ivar = np.ones(arc.shape) log.warning("found only %d HDU in arc, do not use ivar"%len(arc_hdu)) header = arc_hdu[0].header ny = arc.shape[0] ##################################### # Extract arc spectra (one per fiber) log.info("Extracting arcs") if xfit is None: wv_array = np.linspace(WAVEMIN, WAVEMAX, num=arc.shape[0]) nfiber = XCOEFF.shape[0] ncoeff = XCOEFF.shape[1] xfit = np.zeros((arc.shape[0], nfiber)) # Generate a fit_dict fit_dict = dufits.mk_fit_dict(XCOEFF[:,0], ncoeff, 'legendre', WAVEMIN, WAVEMAX) for ii in range(nfiber): fit_dict['coeff'] = XCOEFF[ii,:] xfit[:,ii] = dufits.func_val(wv_array, fit_dict) all_spec = desiboot.extract_sngfibers_gaussianpsf(arc, arc_ivar, xfit, gauss) ############################ # Line list camera = header['CAMERA'].lower() log.info("Loading line list") llist = desiboot.load_arcline_list(camera,vacuum=True,lamps=lamps) dlamb, gd_lines = desiboot.load_gdarc_lines(camera,llist,vacuum=True,lamps=lamps,good_lines_filename=args.good_lines) ##################################### # Loop to solve for wavelengths all_wv_soln = [] all_dlamb = [] debug=False id_dict_of_fibers=[] # first loop to find arc lines and do a first matching for ii in range(all_spec.shape[1]): spec = all_spec[:,ii] id_dict={} id_dict["fiber"] = ii id_dict["status"] = "none" id_dict['id_pix'] = [] id_dict['id_idx'] = [] id_dict['id_wave'] = [] pixpk, flux = desiboot.find_arc_lines(spec) id_dict["pixpk"] = pixpk id_dict["flux"] = flux try: desiboot.id_arc_lines_using_triplets(id_dict, gd_lines, dlamb,ntrack=args.ntrack,nmax=args.nmax,toler=args.toler) except : log.warning(sys.exc_info()) log.warning("fiber {:d} ID_ARC failed".format(ii)) id_dict['status'] = "failed" id_dict_of_fibers.append(id_dict) continue # Add lines if len(id_dict['pixpk'])>len(id_dict['id_pix']) : desiboot.id_remainder(id_dict, llist, deg=args.legendre_degree) log.info("Fiber #{:d} n_match={:d} n_detec={:d}".format(ii,len(id_dict['id_pix']),len(id_dict['pixpk']))) # Save id_dict_of_fibers.append(id_dict) # now record the list of waves identified in several fibers matched_lines=np.array([]) for ii in range(all_spec.shape[1]): matched_lines = np.append(matched_lines,id_dict_of_fibers[ii]['id_wave']) matched_lines = np.unique(matched_lines) number_of_detections = [] for line in matched_lines : ndet=0 for ii in range(all_spec.shape[1]): if np.sum(id_dict_of_fibers[ii]['id_wave']==line) >0 : ndet += 1 print(line,"ndet=",ndet) number_of_detections.append(ndet) # choose which lines are ok and # ok if 5 detections (coincidental error very low) min_number_of_detections=min(5,all_spec.shape[1]) number_of_detections=np.array(number_of_detections) good_matched_lines = matched_lines[number_of_detections>=min_number_of_detections] bad_matched_lines = matched_lines[number_of_detections<min_number_of_detections] log.info("good matched lines = {:s}".format(str(good_matched_lines))) log.info("bad matched lines = {:s}".format(str(bad_matched_lines))) # loop again on all fibers for ii in range(all_spec.shape[1]): spec = all_spec[:,ii] id_dict = id_dict_of_fibers[ii] n_matched_lines=len(id_dict['id_wave']) n_detected_lines=len(id_dict['pixpk']) # did we find any bad line for this fiber? n_bad = np.intersect1d(id_dict['id_wave'],bad_matched_lines).size # how many good lines did we find n_good = np.intersect1d(id_dict['id_wave'],good_matched_lines).size if id_dict['status']=="ok" and ( n_bad>0 or (n_good < good_matched_lines.size-1 and n_good<30) ) and n_good<40 : log.info("Try to refit fiber {:d} with n_bad={:d} and n_good={:d} when n_good_all={:d} n_detec={:d}".format(ii,n_bad,n_good,good_matched_lines.size,n_detected_lines)) try: desiboot.id_arc_lines_using_triplets(id_dict, good_matched_lines, dlamb,ntrack=args.ntrack,nmax=args.nmax) except: log.warning(sys.exc_info()) log.warning("ID_ARC failed on fiber {:d}".format(ii)) id_dict["status"]="failed" if id_dict['status']=="ok" and len(id_dict['pixpk'])>len(id_dict['id_pix']) : desiboot.id_remainder(id_dict, llist, deg=args.legendre_degree) else : log.info("Do not refit fiber {:d} with n_bad={:d} and n_good={:d} when n_good_all={:d} n_detec={:d}".format(ii,n_bad,n_good,good_matched_lines.size,n_detected_lines)) if id_dict['status'] != 'ok': all_wv_soln.append(id_dict) all_dlamb.append(0.) log.warning("Fiber #{:d} failed, no final fit".format(ii)) continue # Final fit wave vs. pix too id_wave=np.array(id_dict['id_wave']) id_pix=np.array(id_dict['id_pix']) deg=max(1,min(args.legendre_degree,id_wave.size-2)) final_fit, mask = dufits.iter_fit(id_wave,id_pix, 'polynomial', deg, xmin=0., xmax=1., sig_rej=3.) rms = np.sqrt(np.mean((dufits.func_val(id_wave[mask==0], final_fit)-id_pix[mask==0])**2)) final_fit_pix,mask2 = dufits.iter_fit(id_pix[mask==0],id_wave[mask==0],'legendre',deg , sig_rej=100000000.) rms_pix = np.sqrt(np.mean((dufits.func_val(id_pix[mask==0], final_fit_pix)-id_wave[mask==0])**2)) # Append wave = dufits.func_val(np.arange(spec.size),final_fit_pix) idlamb = np.median(np.abs(wave-np.roll(wave,1))) all_dlamb.append(idlamb) # Save id_dict['final_fit'] = final_fit id_dict['rms'] = rms id_dict['final_fit_pix'] = final_fit_pix id_dict['wave_min'] = dufits.func_val(0,final_fit_pix) id_dict['wave_max'] = dufits.func_val(ny-1,final_fit_pix) id_dict['mask'] = mask log.info("Fiber #{:d} final fit rms(y->wave) = {:g} A ; rms(wave->y) = {:g} pix ; nlines = {:d}".format(ii,rms,rms_pix,id_pix.size)) all_wv_soln.append(id_dict) if QA: desiboot.qa_arc_spec(all_spec, all_wv_soln, pp) desiboot.qa_fiber_arcrms(all_wv_soln, pp) desiboot.qa_fiber_dlamb(all_spec, all_wv_soln, pp) else: all_wv_soln = None ########### # Write PSF file log.info("Writing PSF file") desiboot.write_psf(args.outfile, xfit, fdicts, gauss, all_wv_soln, legendre_deg=args.legendre_degree , without_arc=args.trace_only, XCOEFF=XCOEFF,fiberflat_header=contfile_header,arc_header=arc_header) log.info("Successfully wrote {:s}".format(args.outfile)) if ( not args.trace_only ) and args.out_line_list : log.info("Writing list of lines found in {:s}".format(args.out_line_list)) desiboot.write_line_list(args.out_line_list,all_wv_soln,llist) log.info("Successfully wrote {:s}".format(args.out_line_list)) ########### # All done if QA: log.info("Successfully wrote {:s}".format(args.qafile)) pp.close() log.info("end") return