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Fix quickquasars targetid truth #457

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merged 9 commits into from Dec 4, 2018
Merged

Fix quickquasars targetid truth #457

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84d02c1
fix TARGETID to its value in metadat
londumas Dec 3, 2018
54746cb
add TARGETID to DLA and BAL
londumas Dec 3, 2018
35d4c7f
Save DZ_SYS and DZ_STAT in truth
londumas Dec 3, 2018
39939a5
Correct fir pixels between north and south
londumas Dec 3, 2018
43de8c2
change TRUEZ to Z and add Z_INPUT
londumas Dec 4, 2018
f4f5a54
Update doc
londumas Dec 4, 2018
1d12146
Add TRUEZ
londumas Dec 4, 2018
705c033
change sigma to gamma
londumas Dec 4, 2018
9e67514
comput the redshift shift from the iput redshift
londumas Dec 4, 2018
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45 changes: 24 additions & 21 deletions py/desisim/scripts/quickquasars.py
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Expand Up @@ -359,24 +359,22 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
for ii in range(len(metadata)):

# quasars with z < min_z will not have any DLA in spectrum
if min_lya_z > metadata[ii]['Z']:
continue
if min_lya_z>metadata['Z'][ii]: continue

# quasar ID
idd=metadata['MOCKID'][ii]
dlas=[]

if args.dla=='file':

for dla in dla_info[dla_info['MOCKID']==idd]:

# Adding only DLAs with z < zqso
if (dla['Z_DLA']< metadata[ii]['Z']):
dlas.append(dict(z=dla['Z_DLA']+dla['DZ_DLA'],N=dla['N_HI_DLA']))
if dla['Z_DLA']>=metadata['Z'][ii]: continue
dlas.append(dict(z=dla['Z_DLA']+dla['DZ_DLA'],N=dla['N_HI_DLA']))
transmission_dla = dla_spec(trans_wave,dlas)

elif args.dla=='random':

dlas, transmission_dla = insert_dlas(trans_wave, metadata[ii]['Z'], rstate=random_state_just_for_dlas)
dlas, transmission_dla = insert_dlas(trans_wave, metadata['Z'][ii], rstate=random_state_just_for_dlas)

# multiply transmissions and store information for the DLA file
if len(dlas)>0:
Expand All @@ -388,9 +386,9 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
# write file with DLA information
if len(dla_id)>0:
dla_meta=Table()
dla_meta['NHI']=dla_NHI
dla_meta['z']=dla_z
dla_meta['ID']=dla_id
dla_meta['NHI'] = dla_NHI
dla_meta['Z'] = dla_z
dla_meta['TARGETID'] = dla_id

hdu_dla = pyfits.convenience.table_to_hdu(dla_meta)
hdu_dla.name="DLA_META"
Expand Down Expand Up @@ -462,6 +460,8 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
lyaforest=False, nocolorcuts=True,
noresample=True, seed=seed, south=issouth)

_meta['TARGETID'][:] = metadata['MOCKID']
_qsometa['TARGETID'][:] = metadata['MOCKID']
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Those two lines are what fixes the original bug?

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Yes, it is. Plus some other for DLA and BAL.

meta[these] = _meta
qsometa[these] = _qsometa
tmp_qso_flux[these, :] = _tmp_qso_flux
Expand Down Expand Up @@ -492,6 +492,9 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
# restore random state to get the same random numbers later
# as when we don't insert BALs
np.random.set_state(rnd_state)
meta_bal['TARGETID'] = metadata['MOCKID']
w = meta_bal['TEMPLATEID']!=-1
meta_bal = meta_bal[:][w]
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hdu_bal=pyfits.convenience.table_to_hdu(meta_bal); hdu_bal.name="BAL_META"
del meta_bal
else:
Expand Down Expand Up @@ -606,7 +609,7 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
meta=specmeta,seed=seed,fibermap_columns=fibermap_columns,use_poisson=False) # use Poisson = False to get reproducible results.


##Adedd to write the truth file, includen metadata for DLA's and BALs
##Adedd to write the truth file, includen metadata for DLA's and BALs
log.info('Writing a truth file {}'.format(truth_filename))
meta.rename_column('REDSHIFT','TRUEZ')
meta.add_column(Column(Z_noFOG,name='TRUEZ_noFOG'))
Expand All @@ -624,9 +627,9 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
hduqso.header['EXTNAME'] = 'QSO_META'
hdulist=pyfits.HDUList([pyfits.PrimaryHDU(),hdu,hduqso])
if args.dla:
hdulist.append(hdu_dla)
hdulist.append(hdu_dla)
if args.balprob:
hdulist.append(hdu_bal)
hdulist.append(hdu_bal)
hdulist.writeto(truth_filename, overwrite=True)
hdulist.close()

Expand All @@ -649,20 +652,20 @@ def simulate_one_healpix(ifilename,args,model,obsconditions,decam_and_wise_filte
('DELTACHI2', 'f8'),
('BRICKNAME', (str,8))]
zbest = Table(np.zeros(nqso, dtype=columns))
zbest["CHI2"][:] = 0.
zbest["Z"] = metadata['Z']
zbest["ZERR"][:] = 0.
zbest["CHI2"][:] = 0.
zbest["Z"][:] = metadata['Z']
zbest["ZERR"][:] = 0.

if args.gamma_kms_zfit:
log.info("Added zfit error with sigma {} to zbest".format(args.gamma_kms_zfit))
dz_fit=mod_cauchy(loc=0,scale=args.gamma_kms_zfit,size=nqso,cut=3000)*(1.+metadata['Z'])/c
zbest["Z"]+=dz_fit

zbest["ZERR"][:] = 0
zbest["ZWARN"][:] = 0
zbest["SPECTYPE"][:] = "QSO"
zbest["SUBTYPE"][:] = ""
zbest["TARGETID"] = fibermap["TARGETID"]
zbest["ZERR"][:] = 0
zbest["ZWARN"][:] = 0
zbest["SPECTYPE"][:] = 'QSO'
zbest["SUBTYPE"][:] = ''
zbest["TARGETID"][:] = metadata['MOCKID']
zbest["DELTACHI2"][:] = 25.
hzbest = pyfits.convenience.table_to_hdu(zbest); hzbest.name="ZBEST"
hfmap = pyfits.convenience.table_to_hdu(fibermap); hfmap.name="FIBERMAP"
Expand Down