def page_subset_expo(fdir, exposure, frametype, petals, html_dir,
titlepage_prefix, mask, log, nspecperfile, snr_cut):
'''
Running prospect from frames : loop over petals for a given exposure
'''
nspec_done = 0
for petal_num in petals:
frames = [
desispec.io.read_frame(
os.path.join(
fdir, frametype + "-" + band + petal_num + "-" + exposure +
".fits")) for band in ['b', 'r', 'z']
]
spectra = utils_specviewer.frames2spectra(frames, with_scores=True)
if 'FIBERSTATUS' in spectra.fibermap.keys():
spectra = myspecselect.myspecselect(spectra,
clean_fiberstatus=True)
if spectra is None: return 0
# Selection
if (mask != None) or (snr_cut != None):
spectra = utils_specviewer.specviewer_selection(
spectra,
log=log,
mask=mask,
mask_type='CMX_TARGET',
snr_cut=snr_cut,
with_dirty_mask_merge=True)
if spectra == 0: continue
# Handle several html pages per exposure - sort by fiberid
nspec_expo = spectra.num_spectra()
log.info("Petal number " + petal_num + " : " + str(nspec_expo) +
" spectra")
sort_indices = np.argsort(spectra.fibermap["FIBER"])
nbpages = int(np.ceil((nspec_expo / nspecperfile)))
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) * nspecperfile:i_page *
nspecperfile]
thespec = myspecselect.myspecselect(spectra, indices=the_indices)
titlepage = titlepage_prefix + "_petal" + petal_num + "_" + str(
i_page)
plotframes.plotspectra(thespec,
with_noise=True,
with_coaddcam=True,
is_coadded=False,
title=titlepage,
html_dir=html_dir,
mask_type='CMX_TARGET',
with_thumb_only_page=True)
nspec_done += nspec_expo
return nspec_done
def load_spectra_zcat_from_targets(targets, tiledir, obs_db, with_redrock=False, with_redrock_version=True) :
'''
Creates (spectra,zcat,[redrock_cat]) = (Spectra object, zcatalog Table, [redrock Table]) from a list of targetids
- targets must be a list of int64
- obs_db: "mini-db" produced by make_targetdict()
- with_redrock: if True, also get redrock Table
- with_redrock_version: if True, add a Column to zcat with RRVER from hdu0 in zbest files
'''
targets = np.asarray(targets)
if targets.dtype != 'int64' :
raise TypeError('Targetids should be int64.')
spectra = None
ztables, rrtables = [], []
for tile_night in obs_db.keys() :
petals = np.unique(obs_db[tile_night]['petal'])
for petal in petals :
targets_subset = []
for target in targets :
w, = np.where( (obs_db[tile_night]['targetid']==target) & (obs_db[tile_night]['petal']==petal) )
if len(w) == 0 : continue
if len(w) > 1 :
print("Warning ! Several entries in tile/night "+tile_night+" available for target "+str(target))
targets_subset.append(target)
# Load spectra for that tile/night/petal only if there's a target from the list
if len(targets_subset)>0 :
the_path = tile_night.replace("-","/")
the_spec = desispec.io.read_spectra(os.path.join(tiledir,the_path,"coadd-"+petal+"-"+tile_night+".fits"))
the_spec = myspecselect.myspecselect(the_spec, targets=targets_subset, remove_scores=True)
the_zcat = Table.read(os.path.join(tiledir,the_path,"zbest-"+petal+"-"+tile_night+".fits"),'ZBEST')
if with_redrock_version:
hdulist = astropy.io.fits.open(os.path.join(tiledir,the_path,"zbest-"+petal+"-"+tile_night+".fits"))
the_zcat['RRVER'] = hdulist[hdulist.index_of('PRIMARY')].header['RRVER']
the_zcat, dummy = match_zcat_to_spectra(the_zcat, the_spec)
ztables.append(the_zcat)
if with_redrock :
rrfile = os.path.join(tiledir,the_path,"redrock-"+petal+"-"+tile_night+".h5")
the_rrcat = match_redrock_zfit_to_spectra(rrfile, the_spec, Nfit=None)
rrtables.append(the_rrcat)
if spectra is None : spectra = the_spec
else : spectra = myspecupdate.myspecupdate(spectra,the_spec)
# Check if all targets were found in spectra
tids_spectra = spectra.fibermap['TARGETID']
for target in targets :
if target not in tids_spectra : print("Warning! targetid not found: "+str(target))
zcat = vstack(ztables)
if with_redrock :
rrcat = vstack(rrtables)
return (spectra, zcat, rrcat)
else :
return (spectra,zcat)
def load_spectra_zcat_from_targets(targets, tiledir, obs_db):
'''
Creates (spectra,zcat) = (Spectra object, zcatalog Table) from a list of targetids
- targets must be a list of int64
- obs_db : "mini-db" produced by make_targetdict()
'''
spectra = None
ztables = []
for target in targets:
for tile_night in obs_db.keys():
w, = np.where(obs_db[tile_night]['targetid'] == target)
if len(w) > 1:
print("Warning ! Several entries in tile/night " + tile_night +
" available for target " + str(target))
if len(w) == 0: continue
the_path = tile_night.replace("-", "/")
the_petal = obs_db[tile_night]['petal'][w[0]]
the_spec = desispec.io.read_spectra(
os.path.join(tiledir, the_path, "coadd-" + the_petal + "-" +
tile_night + ".fits"))
the_spec = myspecselect.myspecselect(the_spec,
targets=[target],
remove_scores=True)
if the_spec.num_spectra() != 1:
print("Warning ! Several spectra for " + tile_night +
" and target " + str(target))
the_zcat = Table.read(
os.path.join(tiledir, the_path, "zbest-" + the_petal + "-" +
tile_night + ".fits"), 'ZBEST')
the_zcat, dummy = match_zcat_to_spectra(the_zcat, the_spec)
ztables.append(the_zcat)
if spectra is None: spectra = the_spec
else: spectra = myspecupdate.myspecupdate(spectra, the_spec)
zcat = vstack(ztables)
return (spectra, zcat)
def page_subset_tile(fdir, tile_db_subset, frametype, html_dir,
titlepage_prefix, mask, log, nspecperfile, snr_cut):
'''
Running prospect from frames : tile-based, do not separate pages per exposure.
tile_db_subset : subset of tile_db, all with the same tile
'''
tile = tile_db_subset['tile']
nspec_done = 0
all_spectra = None
for the_subset in tile_db_subset['db_subset']:
assert (the_subset['tile'] == tile)
log.info("Tile " + tile + " : reading frames from exposure " +
the_subset['exposure'])
for spectrograph_num in the_subset['spectrographs']:
frames = [
desispec.io.read_frame(
os.path.join(
fdir, the_subset['night'],
frametype + "-" + band + spectrograph_num + "-" +
the_subset['exposure'] + ".fits"))
for band in ['b', 'r', 'z']
]
### TMP TRICK (?) : need to have exposures in fibermaps, otherwise spectra.update() crashes !
for fr in frames:
if not ('EXPID' in fr.fibermap.keys()):
fr.fibermap['EXPID'] = fr.fibermap['FIBER']
for i in range(len(fr.fibermap)):
fr.fibermap['EXPID'][i] = the_subset['exposure']
### END TMP TRICK
### OTHER TRICK : need resolution data in spectra to pass coadd fct (could be changed...)
spectra = utils_specviewer.frames2spectra(
frames, with_scores=True, with_resolution_data=True)
# Filtering
if (mask != None) or (snr_cut != None):
spectra = utils_specviewer.specviewer_selection(
spectra,
log=log,
mask=mask,
mask_type='CMX_TARGET',
snr_cut=snr_cut)
if spectra == 0: continue
# Merge
if all_spectra is None:
all_spectra = spectra
else:
all_spectra.update(
spectra
) # NB update() does not copy scores. Filtering was done before.
if all_spectra is None:
log.info("Tile " + tile + " : no spectra !")
return 0
# Exposure-coadd
all_spectra = utils_specviewer.coadd_targets(all_spectra)
# Handle several html pages per exposure - sort by targetid
nspec_tile = all_spectra.num_spectra()
log.info("Tile " + tile + " : " + str(nspec_tile) +
" exposure-coadded spectra")
sort_indices = np.argsort(all_spectra.fibermap["TARGETID"])
nbpages = int(np.ceil((nspec_tile / nspecperfile)))
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) * nspecperfile:i_page *
nspecperfile]
thespec = myspecselect.myspecselect(all_spectra, indices=the_indices)
titlepage = titlepage_prefix + "_" + str(i_page)
plotframes.plotspectra(thespec,
with_noise=True,
with_coaddcam=True,
is_coadded=True,
title=titlepage,
html_dir=html_dir,
mask_type='CMX_TARGET',
with_thumb_only_page=True)
nspec_done += nspec_tile
return nspec_done
def specviewer_selection(spectra,
log=None,
mask=None,
mask_type=None,
gmag_cut=None,
rmag_cut=None,
chi2cut=None,
zbest=None,
snr_cut=None,
with_dirty_mask_merge=False,
remove_scores=False):
'''
Simple sub-selection on spectra based on meta-data.
Implemented cuts based on : target mask ; photo mag (g, r) ; chi2 from fit ; SNR (in spectra.scores, BRZ)
- if chi2cut : a catalog zbest must be provided, with entries matching exactly those of spectra
'''
# SNR selection
if snr_cut is not None:
assert ((len(snr_cut) == 2) and (spectra.scores is not None))
for band in ['B', 'R', 'Z']:
w, = np.where(
(spectra.scores['MEDIAN_CALIB_SNR_' + band] > snr_cut[0])
& (spectra.scores['MEDIAN_CALIB_SNR_' + band] < snr_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with MEDIAN_CALIB_SNR_" + band +
" in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(
spectra, targets=targetids, remove_scores=remove_scores)
# Target mask selection
if mask is not None:
assert mask_type in ['SV1_DESI_TARGET', 'DESI_TARGET', 'CMX_TARGET']
if mask_type == 'SV1_DESI_TARGET':
assert (mask in sv1_desi_mask.names())
w, = np.where(
(spectra.fibermap['SV1_DESI_TARGET'] & sv1_desi_mask[mask]))
elif mask_type == 'DESI_TARGET':
assert (mask in desi_mask.names())
w, = np.where((spectra.fibermap['DESI_TARGET'] & desi_mask[mask]))
elif mask_type == 'CMX_TARGET':
assert (mask in cmx_mask.names())
mask2 = None
if with_dirty_mask_merge: # Self-explanatory... only for fast VI of minisv
if mask in ['SV0_QSO', 'SV0_ELG', 'SV0_LRG']:
mask2 = mask.replace('SV0', 'MINI_SV')
if mask == 'SV0_BGS': mask2 = 'MINI_SV_BGS_BRIGHT'
if mask in ['SV0_STD_FAINT', 'SV0_STD_BRIGHT']:
mask2 = mask.replace('SV0_', '')
if mask2 is None:
w, = np.where(
(spectra.fibermap['CMX_TARGET'] & cmx_mask[mask]))
else:
w, = np.where((spectra.fibermap['CMX_TARGET'] & cmx_mask[mask])
| (spectra.fibermap['CMX_TARGET']
& cmx_mask[mask2]))
if len(w) == 0:
if log is not None: log.info(" * No spectra with mask " + mask)
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra,
targets=targetids,
remove_scores=remove_scores)
# Photometry selection
if gmag_cut is not None:
assert len(gmag_cut) == 2 # Require range [gmin, gmax]
gmag = np.zeros(spectra.num_spectra())
w, = np.where((spectra.fibermap['FLUX_G'] > 0)
& (spectra.fibermap['MW_TRANSMISSION_G'] > 0))
gmag[w] = -2.5 * np.log10(
spectra.fibermap['FLUX_G'][w] /
spectra.fibermap['MW_TRANSMISSION_G'][w]) + 22.5
w, = np.where((gmag > gmag_cut[0]) & (gmag < gmag_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with g_mag in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
if rmag_cut is not None:
assert len(rmag_cut) == 2 # Require range [rmin, rmax]
rmag = np.zeros(spectra.num_spectra())
w, = np.where((spectra.fibermap['FLUX_R'] > 0)
& (spectra.fibermap['MW_TRANSMISSION_R'] > 0))
rmag[w] = -2.5 * np.log10(
spectra.fibermap['FLUX_R'][w] /
spectra.fibermap['MW_TRANSMISSION_R'][w]) + 22.5
w, = np.where((rmag > rmag_cut[0]) & (rmag < rmag_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with r_mag in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra,
targets=targetids,
remove_scores=remove_scores)
# Chi2 selection
if chi2cut is not None:
assert len(chi2cut) == 2 # Require range [chi2min, chi2max]
if np.any(zbest['TARGETID'] != spectra.fibermap['TARGETID']):
raise RunTimeError(
'specviewer_selection : zbest and spectra do not match (different targetids)'
)
w, = np.where((zbest['DELTACHI2'] > chi2cut[0])
& (zbest['DELTACHI2'] < chi2cut[1]))
if len(w) == 0:
if log is not None:
log.info(
" * No target in this pixel with DeltaChi2 in requested range"
)
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra,
targets=targetids,
remove_scores=remove_scores)
return spectra
def main(args):
log = get_logger()
specprod_dir = args.specprod_dir
if specprod_dir is None: specprod_dir = desispec.io.specprod_root()
webdir = args.webdir
if webdir is None:
webdir = os.environ[
"DESI_WWW"] + "/users/armengau/svdc2019c" # TMP, for test
nights = desispec.io.get_nights(specprod_dir=specprod_dir)
# TODO - Select night (eg. only last night)
nights = nights[8:11] # TMP, for test
for thenight in nights:
# Get spectra from tiles dir - To consolidate
specfiles = glob.glob(
os.path.join(specprod_dir,
"tiles/*/tilespectra-*-" + thenight + ".fits"))
for f in specfiles:
log.info("Working on file " + f)
file_label = f[
f.find("tilespectra-") + 12:f.find(thenight) -
1] # From tile-based file description - To consolidate
spectra = desispec.io.read_spectra(f)
zbfile = f.replace("tilespectra", "zbest")
zbest = Table.read(zbfile, 'ZBEST')
# Handle several html pages per pixel : sort by TARGETID
# NOTE : this way, individual spectra from the same target are together
# Does it make sense ? (they have the same fit)
nbpages = int(np.ceil((spectra.num_spectra() / args.nspecperfile)))
sort_indices = np.argsort(
spectra.fibermap["TARGETID"],
kind='mergesort') # keep order of equal elts
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) *
args.nspecperfile:i_page *
args.nspecperfile]
thespec = myspecselect.myspecselect(spectra,
indices=the_indices)
thezb, kk = utils_specviewer.match_zcat_to_spectra(
zbest, thespec)
model = plotframes.create_model(thespec, thezb)
### No VI results to display by default
# vifile = os.environ['HOME']+"/prospect/vilist_prototype.fits"
# vidata = utils_specviewer.match_vi_targets(vifile, thespec.fibermap["TARGETID"])
titlepage = "specviewer_night" + thenight + "_" + file_label + "_" + str(
i_page)
html_dir = webdir + "/nights/night" + thenight
if not os.path.exists(html_dir):
os.makedirs(html_dir)
os.mkdir(html_dir + "/vignettes")
plotframes.plotspectra(thespec,
zcatalog=thezb,
vidata=None,
model=model,
title=titlepage,
html_dir=html_dir,
is_coadded=False)
for i_spec in range(thespec.num_spectra()):
saveplot = html_dir + "/vignettes/night" + thenight + "_" + file_label + "_" + str(
i_page) + "_" + str(i_spec) + ".png"
utils_specviewer.miniplot_spectrum(
thespec,
i_spec,
model=model,
saveplot=saveplot,
smoothing=args.vignette_smoothing)
def page_subset_tile(fdir,
tile_db_subset,
frametype,
html_dir,
titlepage_prefix,
mask,
log,
nspecperfile,
snr_cut,
with_zcatalog=False):
'''
Running prospect from frames : tile-based, do not separate pages per exposure.
tile_db_subset : subset of tile_db, all with the same tile
'''
tile = tile_db_subset['tile']
nspec_done = 0
all_spectra = None
for the_subset in tile_db_subset['db_subset']:
assert (the_subset['tile'] == tile)
log.info("Tile " + tile + " : reading frames from exposure " +
the_subset['exposure'])
for petal_num in the_subset['petals']:
frames = [
desispec.io.read_frame(
os.path.join(
fdir, the_subset['night'], frametype + "-" + band +
petal_num + "-" + the_subset['exposure'] + ".fits"))
for band in ['b', 'r', 'z']
]
# TRICK : need resolution data in spectra to pass coadd fct (could be changed...)
spectra = utils_specviewer.frames2spectra(
frames, with_scores=True, with_resolution_data=True)
# Filtering
if (mask != None) or (snr_cut != None):
spectra = utils_specviewer.specviewer_selection(
spectra,
log=log,
mask=mask,
mask_type='CMX_TARGET',
snr_cut=snr_cut,
with_dirty_mask_merge=True)
if spectra == 0: continue
# Merge
if all_spectra is None:
all_spectra = spectra
else: # NB update() does not copy scores. Filtering was done before.
all_spectra = myspecupdate.myspecupdate(all_spectra, spectra)
if all_spectra is None:
log.info("Tile " + tile + " : no spectra !")
return 0
elif 'FIBERSTATUS' in all_spectra.fibermap.keys():
all_spectra = myspecselect.myspecselect(all_spectra,
clean_fiberstatus=True,
remove_scores=True)
if all_spectra is None: return 0
# Exposure-coadd
all_spectra = utils_specviewer.coadd_targets(all_spectra)
# zcatalog
if with_zcatalog:
zcat_files = glob.glob(fdir + "/" + the_subset['night'] +
"/zbest*.fits") # Probably TMP ... ?
ztables = []
for f in zcat_files:
ztables.append(Table.read(f, 'ZBEST'))
zcat = vstack(ztables)
else:
zcat = None
# Handle several html pages per exposure - sort by targetid
nspec_tile = all_spectra.num_spectra()
log.info("Tile " + tile + " : " + str(nspec_tile) +
" exposure-coadded spectra")
sort_indices = np.argsort(all_spectra.fibermap["TARGETID"])
nbpages = int(np.ceil((nspec_tile / nspecperfile)))
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) * nspecperfile:i_page *
nspecperfile]
thespec = myspecselect.myspecselect(all_spectra,
indices=the_indices,
remove_scores=True)
titlepage = titlepage_prefix + "_" + str(i_page)
plotframes.plotspectra(thespec,
with_noise=True,
with_coaddcam=True,
is_coadded=True,
zcatalog=zcat,
title=titlepage,
html_dir=html_dir,
mask_type='CMX_TARGET',
with_thumb_only_page=True)
nspec_done += nspec_tile
return nspec_done
def main(args):
log = get_logger()
specprod_dir = args.specprod_dir
if specprod_dir is None: specprod_dir = desispec.io.specprod_root()
webdir = args.webdir
if webdir is None:
webdir = os.environ[
"DESI_WWW"] + "/users/armengau/svdc2019c" # TMP, for test
# TODO - Selection on pixels based on existing specviewer pages
if args.pixel_list is None:
pixels = glob.glob(os.path.join(specprod_dir, "spectra-64/*/*"))
pixels = [x[x.rfind("/") + 1:] for x in pixels]
else:
pixels = np.loadtxt(args.pixel_list, dtype=str)
if args.random_pixels:
random.shuffle(pixels)
# Loop on pixels
nspec_done = 0
for pixel in pixels:
log.info("Working on pixel " + pixel)
thefile = desispec.io.findfile('spectra',
groupname=int(pixel),
specprod_dir=specprod_dir)
individual_spectra = desispec.io.read_spectra(thefile)
spectra = plotframes.coadd_targets(individual_spectra)
zbfile = thefile.replace('spectra-64-', 'zbest-64-')
if os.path.isfile(zbfile):
zbest = Table.read(zbfile, 'ZBEST')
else:
log.info("No associated zbest file found : skipping pixel")
continue
spectra = utils_specviewer.specviewer_selection(
spectra,
log=log,
mask=args.mask,
mask_type=args.mask_type,
gmag_cut=args.gcut,
rmag_cut=args.rcut,
chi2cut=args.chi2cut,
zbest=zbest)
if spectra == 0: continue
# Handle several html pages per pixel : sort by TARGETID
# TODO - Find a more useful sort ?
nbpages = int(np.ceil((spectra.num_spectra() / args.nspecperfile)))
sort_indices = np.argsort(spectra.fibermap["TARGETID"])
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) *
args.nspecperfile:i_page *
args.nspecperfile]
thespec = myspecselect.myspecselect(spectra, indices=the_indices)
thezb, kk = utils_specviewer.match_zcat_to_spectra(zbest, thespec)
### No VI results to display by default
# VI "catalog" - location to define later ..
# vifile = os.environ['HOME']+"/prospect/vilist_prototype.fits"
# vidata = utils_specviewer.match_vi_targets(vifile, thespec.fibermap["TARGETID"])
titlepage = "pix" + pixel + "_" + str(i_page)
if args.gcut is not None:
titlepage = "gcut-" + str(args.gcut[0]) + "-" + str(
args.gcut[1]) + "_" + titlepage
if args.rcut is not None:
titlepage = "rcut-" + str(args.rcut[0]) + "-" + str(
args.rcut[1]) + "_" + titlepage
if args.chi2cut is not None:
titlepage = "chi2cut-" + str(args.chi2cut[0]) + "-" + str(
args.chi2cut[1]) + "_" + titlepage
if args.mask is not None:
titlepage = args.mask + "_" + titlepage
model = plotframes.create_model(thespec, thezb)
html_dir = os.path.join(webdir, "pix" + pixel)
if not os.path.exists(html_dir):
os.makedirs(html_dir)
os.mkdir(html_dir + "/vignettes")
plotframes.plotspectra(thespec,
zcatalog=zbest,
model_from_zcat=True,
vidata=None,
model=None,
title=titlepage,
html_dir=html_dir,
is_coadded=True,
mask_type=args.mask_type)
# for i_spec in range(thespec.num_spectra()) :
# saveplot = html_dir+"/vignettes/pix"+pixel+"_"+str(i_page)+"_"+str(i_spec)+".png"
# utils_specviewer.miniplot_spectrum(thespec, i_spec, model=model, saveplot=saveplot, smoothing = args.vignette_smoothing)
nspec_done += thespec.num_spectra()
# Stop running if needed, only once a full pixel is completed
if args.nmax_spectra is not None:
if nspec_done >= args.nmax_spectra:
log.info(
str(nspec_done) +
" spectra done : no other pixel will be processed")
break
def specviewer_selection(spectra,
log=None,
mask=None,
mask_type=None,
gmag_cut=None,
rmag_cut=None,
chi2cut=None,
zbest=None,
snr_cut=None):
'''
Simple sub-selection on spectra based on meta-data.
Implemented cuts based on : target mask ; photo mag (g, r) ; chi2 from fit ; SNR (in spectra.scores, BRZ)
'''
# Target mask selection
if mask is not None:
assert mask_type in ['SV1_DESI_TARGET', 'DESI_TARGET', 'CMX_TARGET']
if mask_type == 'SV1_DESI_TARGET':
assert (mask in sv1_desi_mask.names())
w, = np.where(
(spectra.fibermap['SV1_DESI_TARGET'] & sv1_desi_mask[mask]))
elif mask_type == 'DESI_TARGET':
assert (mask in desi_mask.names())
w, = np.where((spectra.fibermap['DESI_TARGET'] & desi_mask[mask]))
elif mask_type == 'CMX_TARGET':
assert (mask in cmx_mask.names())
w, = np.where((spectra.fibermap['CMX_TARGET'] & cmx_mask[mask]))
if len(w) == 0:
if log is not None: log.info(" * No spectra with mask " + mask)
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
# Photometry selection
if gmag_cut is not None:
assert len(gmag_cut) == 2 # Require range [gmin, gmax]
gmag = np.zeros(spectra.num_spectra())
w, = np.where((spectra.fibermap['FLUX_G'] > 0)
& (spectra.fibermap['MW_TRANSMISSION_G'] > 0))
gmag[w] = -2.5 * np.log10(
spectra.fibermap['FLUX_G'][w] /
spectra.fibermap['MW_TRANSMISSION_G'][w]) + 22.5
w, = np.where((gmag > gmag_cut[0]) & (gmag < gmag_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with g_mag in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
if rmag_cut is not None:
assert len(rmag_cut) == 2 # Require range [rmin, rmax]
rmag = np.zeros(spectra.num_spectra())
w, = np.where((spectra.fibermap['FLUX_R'] > 0)
& (spectra.fibermap['MW_TRANSMISSION_R'] > 0))
rmag[w] = -2.5 * np.log10(
spectra.fibermap['FLUX_R'][w] /
spectra.fibermap['MW_TRANSMISSION_R'][w]) + 22.5
w, = np.where((rmag > rmag_cut[0]) & (rmag < rmag_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with r_mag in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
# SNR selection ## TODO check it !! May not work ...
if snr_cut is not None:
assert ((len(snr_cut) == 2) and (spectra.scores is not None))
for band in ['B', 'R', 'Z']:
w, = np.where(
(spectra.scores['MEDIAN_CALIB_SNR_' + band] > snr_cut[0])
& (spectra.scores['MEDIAN_CALIB_SNR_' + band] < snr_cut[1]))
if len(w) == 0:
if log is not None:
log.info(" * No spectra with MEDIAN_CALIB_SNR_" + band +
" in requested range")
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
# Chi2 selection
if chi2cut is not None:
assert len(chi2cut) == 2 # Require range [chi2min, chi2max]
assert (zbest is not None)
thezb, kk = match_zcat_to_spectra(zbest, spectra)
w, = np.where((thezb['DELTACHI2'] > chi2cut[0])
& (thezb['DELTACHI2'] < chi2cut[1]))
if len(w) == 0:
if log is not None:
log.info(
" * No target in this pixel with DeltaChi2 in requested range"
)
return 0
else:
targetids = spectra.fibermap['TARGETID'][w]
spectra = myspecselect.myspecselect(spectra, targets=targetids)
return spectra
def page_subset_tile(fdir,
tile_db_subset,
html_dir,
titlepage_prefix,
mask,
log,
nspecperfile,
snr_cut,
with_zcatalog=False,
template_dir=None,
clean_bad_fibers_cmx=False):
'''
Running prospect from coadds.
'''
tile = tile_db_subset['tile']
night = tile_db_subset['night']
nspec_done = 0
all_spectra = None
log.info("Tile " + tile + " : reading coadds from night " + night)
for petal_num in tile_db_subset['petals']:
fname = os.path.join(
fdir, "coadd-" + petal_num + "-" + tile + '-' + night + ".fits")
spectra = desispec.io.read_spectra(fname)
# Filtering
if (mask != None) or (snr_cut != None):
spectra = utils_specviewer.specviewer_selection(
spectra,
log=log,
mask=mask,
mask_type='CMX_TARGET',
snr_cut=snr_cut,
with_dirty_mask_merge=True)
if spectra == 0: continue
# Merge
if all_spectra is None:
all_spectra = spectra
else:
# NB update() does not copy scores. Score-based filtering (SNR) was done before.
all_spectra = myspecupdate.myspecupdate(all_spectra, spectra)
if all_spectra is None:
log.info("Tile " + tile + " - night " + night + ": no spectra.")
return 0
else:
clean_fiberstatus = True if 'FIBERSTATUS' in all_spectra.fibermap.keys(
) else False
fibers = None
if clean_bad_fibers_cmx:
fibers = np.arange(5000)
for cut_fiber_range in _bad_fibers_cmx:
fibers = fibers[((fibers < cut_fiber_range[0]) |
(fibers > cut_fiber_range[1]))]
all_spectra = myspecselect.myspecselect(
all_spectra,
clean_fiberstatus=clean_fiberstatus,
fibers=fibers,
remove_scores=True)
if all_spectra is None: return 0
# zcatalog
if with_zcatalog:
ztables = []
for petal_num in tile_db_subset['petals']:
fname = os.path.join(
fdir,
"zbest-" + petal_num + "-" + tile + '-' + night + ".fits")
ztables.append(Table.read(fname, 'ZBEST'))
zcat = vstack(ztables)
else:
zcat = None
# Create several html pages : sort by targetid
nspec_tile = all_spectra.num_spectra()
log.info("Tile " + tile + " - night " + night + ": " + str(nspec_tile) +
" exposure-coadded spectra")
sort_indices = np.argsort(all_spectra.fibermap["TARGETID"])
nbpages = int(np.ceil((nspec_tile / nspecperfile)))
for i_page in range(1, 1 + nbpages):
log.info(" * Page " + str(i_page) + " / " + str(nbpages))
the_indices = sort_indices[(i_page - 1) * nspecperfile:i_page *
nspecperfile]
thespec = myspecselect.myspecselect(all_spectra,
indices=the_indices,
remove_scores=True)
the_zcat, kk = utils_specviewer.match_zcat_to_spectra(zcat, thespec)
titlepage = titlepage_prefix + "_" + str(i_page)
plotframes.plotspectra(thespec,
with_noise=True,
with_coaddcam=False,
is_coadded=True,
zcatalog=the_zcat,
title=titlepage,
html_dir=html_dir,
mask_type='CMX_TARGET',
with_thumb_only_page=True,
template_dir=template_dir)
nspec_done += nspec_tile
return nspec_done