def get_5pops_mass_redshift_bins(self, znodes, mnodes, linear_mass=1):
#pop_suf = ['sf','qt','agn','sb','loc']
self.id_z_ms_5pop = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
if linear_mass == 1:
ind_mz_sf =( (self.table.sfg == 1) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mz_qt =( (self.table.sfg == 0) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mz_agn =( (self.table.sfg == 2) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mz_sb =( (self.table.sfg == 4) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mz_loc=( (self.table.sfg == 3) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
else:
ind_mz_sf =( (self.table.sfg == 1) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
ind_mz_qt =( (self.table.sfg == 0) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
ind_mz_agn =( (self.table.sfg == 2) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
ind_mz_sb =( (self.table.sfg == 4) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
ind_mz_loc=( (self.table.sfg == 3) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
self.id_z_ms_5pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_sf'] = self.table.ID[ind_mz_sf].values
self.id_z_ms_5pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_qt'] = self.table.ID[ind_mz_qt].values
self.id_z_ms_5pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_agn'] = self.table.ID[ind_mz_agn].values
self.id_z_ms_5pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_sb'] = self.table.ID[ind_mz_sb].values
self.id_z_ms_5pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_loc'] = self.table.ID[ind_mz_loc].values
def propagate_predict(modelname, dissimname, predictionsname, outdir=None):
if outdir == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
else:
if not os.path.exists(outdir):
tsh.makedirs(outdir)
args = {}
predictions_meta, predictions = read_listfile(predictionsname)
args.update(predictions_meta)
dissim_meta, sample_ids, dissim = read_weightsfile(dissimname)
assert (predictions['id'] == np.array(sample_ids)).all()
assert predictions_meta['input_name'] == dissim_meta['input_name'], \
'Expecting same input names (%s x %s)' % (predictions_meta['input_name'], dissim_meta['input_name'])
inputname = predictions_meta['input_name']
args.update(dissim_meta)
model = read_propagatorfile(modelname)
args.update(model['meta'])
method_name = model['propagator']['method_name']
del model['propagator']['method_name']
args.update(model['propagator'])
args, prop = propagate(method_name,
args,
predictions,
dissim,
output_dir=outdir)
clean_args(args)
del args['cv_results']
write_listfile(os.path.join(outdir, inputname + '-propagated.csv.gz'),
prop, **args)
def classifier_predict(listname, modelname, outdir=None, n_jobs=None):
if outdir == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
else:
if not os.path.exists(outdir):
tsh.makedirs(outdir)
inputname = os.path.splitext(os.path.basename(listname))[0]
if listname.endswith('.gz'):
inputname = os.path.splitext(inputname)[0]
meta, data = read_listfile(listname)
classifier = read_classifierfile(modelname)
feature_method = classifier['features']['meta']['feature_method']
feature_args = meta.copy()
# Training input_name would shadow the current one.
del classifier['features']['meta']['input_name']
featurename = os.path.join(outdir, inputname + '-feats.csv.gz')
if os.path.exists(featurename):
_, features = read_listfile(featurename)
else:
feature_args.update(classifier['features']['meta'])
args, features = compute_features(feature_method, feature_args, data,
input_name=inputname, n_jobs=n_jobs, output_dir=outdir)
assert (data['id'] == features['id']).all()
clean_args(args)
write_listfile(featurename, features, input_name=inputname, **args)
labels_name = classifier['meta']['truth'] + '_labels'
labels = classifier['meta'][labels_name]
pred = predict(classifier['classifier'], sorted(labels.keys()), features,
output_dir=outdir)
write_listfile(os.path.join(outdir, inputname + '-predictions.csv.gz'), pred,
classifier_name=modelname, truth=classifier['meta']['truth'],
labels_name=labels, input_name=inputname)
def dissimilarities(methodname,
listname,
argsname=None,
n_jobs=None,
outdir=None):
if outdir == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
else:
if not os.path.exists(outdir):
tsh.makedirs(outdir)
inputname = os.path.splitext(os.path.basename(listname))[0]
if listname.endswith('.gz'):
inputname = os.path.splitext(inputname)[0]
meta, data = read_listfile(listname)
args = meta
if argsname != None:
args.update(read_argsfile(argsname))
args, w = compute_dissimilarity(methodname,
args,
data,
n_jobs=n_jobs,
output_dir=outdir,
input_name=inputname)
if 'threshold' in args and args['threshold'] != 'False':
args, w = threshold_dissimilarity(args['threshold'], args, w)
dissim = prepare_weights_data(data['id'], data.dtype['id'], w)
clean_args(args)
write_listfile(os.path.join(outdir, inputname + '-dissim.csv.gz'),
dissim,
input_name=inputname,
**args)
def get_criteria_specific_redshift_bins(self, znodes, mnodes, sfg = 1, criteria = '', crange = [1.0], initialize_pop = False):
pop = ['qt','sf']
nc = len(crange)
if initialize_pop == True: self.id_crit = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
if nc > 1:
for kc in range(len(crange[:-1])):
ind_crit =( (self.table.sfg == sfg) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) &
(clean_nans(self.table[criteria]) >= crange[kc]) & (clean_nans(self.table[criteria]) < crange[kc+1]) )
arg = 'z_'+str('{:.2f}'.format(znodes[iz]))+'_'+str('{:.2f}'.format(znodes[iz+1]))+'__m_'+str('{:.2f}'.format(mnodes[jm]))+'_'+str('{:.2f}'.format(mnodes[jm+1]))+'__'+criteria+'_'+str('{:.2f}'.format(crange[kc],2))+'_'+str('{:.2f}'.format(crange[kc+1],2))+'_'+pop[sfg]
self.id_crit[clean_args(arg)] = self.table.ID[ind_crit].values
else:
#above and below no?
ind_above =( (self.table.sfg == sfg) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) &
(clean_nans(self.table[criteria]) >= crange[0]) )
ind_below =( (self.table.sfg == sfg) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) &
(clean_nans(self.table[criteria]) < crange[0]) )
arg = 'z_'+str('{:.2f}'.format(znodes[iz]))+'_'+str('{:.2f}'.format(znodes[iz+1]))+'__m_'+str('{:.2f}'.format(mnodes[jm]))+'_'+str('{:.2f}'.format(mnodes[jm+1]))+'__'+criteria+'_ge_'+str('{:.2f}'.format(crange[0],2))+'_'+pop[sfg]
self.id_crit[clean_args(arg)] = self.table.ID[ind_above].values
arg = 'z_'+str('{:.2f}'.format(znodes[iz]))+'_'+str('{:.2f}'.format(znodes[iz+1]))+'__m_'+str('{:.2f}'.format(mnodes[jm]))+'_'+str('{:.2f}'.format(mnodes[jm+1]))+'__'+criteria+'_lt_'+str('{:.2f}'.format(crange[0],2))+'_'+pop[sfg]
self.id_crit[clean_args(arg)] = self.table.ID[ind_below].values
def get_general_redshift_bins(self, znodes, mnodes, sfg = 1, suffx = '', Fcut = 25, Ahat = 1.0, initialize_pop = False):
if initialize_pop == True: self.id_z_ms = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
ind_mz =( (self.table.sfg == 1) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
self.id_z_ms['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+suffx] = self.table.ID[ind_mz].values
def get_mass_redshift_bins(self, znodes, mnodes, sfg = 1, pop_suffix = '', initialize_pop = False):
if initialize_pop == True: self.id_z_ms_pop = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
ind_mz =( (self.table.sfg == sfg) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
self.id_z_ms_pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+pop_suffix] = self.table.ID[ind_mz].values
def get_sf_qt_mass_redshift_bins(self, znodes, mnodes):
self.id_z_ms = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
ind_mz_sf =( (self.table.sfg == 1) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mz_qt =( (self.table.sfg == 0) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
self.id_z_ms['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_sf'] = self.table.ID[ind_mz_sf].values
self.id_z_ms['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_qt'] = self.table.ID[ind_mz_qt].values
def get_sf_qt_mass_lookback_time_bins(self, tnodes, mnodes):
self.id_lookt_mass = {}
age_universe = cosmo.age(0).value # 13.797617455819209 Gyr
znodes = np.array([z_at_value(cosmo.age,(age_universe - i) * u.Gyr) for i in tnodes])
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
ind_mt_sf =( (self.table.sfg == 1) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
ind_mt_qt =( (self.table.sfg == 0) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
self.id_lookt_mass['lookt_'+clean_args(str('{:.2f}'.format(tnodes[iz])))+'_'+clean_args(str('{:.2f}'.format(tnodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_sf'] = self.table.ID[ind_mt_sf].values
self.id_lookt_mass['lookt_'+clean_args(str('{:.2f}'.format(tnodes[iz])))+'_'+clean_args(str('{:.2f}'.format(tnodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_qt'] = self.table.ID[ind_mt_qt].values
def get_mass_redshift_uvj_bins(self, znodes, mnodes, cnodes, linear_mass=1):
#pop_suf = ['qt','sf0','sf1','sf2','sf3']
self.id_z_ms_pop = {}
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
for kc in range(len(cnodes)):
if linear_mass == 1:
ind_mz =( (self.table.sfg == kc) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
else:
ind_mz =( (self.table.sfg == kc) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
if kc < len(cnodes)-1: csuf = 'sf'+str(kc)
else: csuf = 'qt'
self.id_z_ms_pop['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_'+csuf] = self.table.ID[ind_mz].values
def __init__(self, action=None, delta=None, when=None, recurring=None, name=None):
if not when and not delta:
raise "Need a time or time span to schedule at"
if not name:
name = action.__name__
if type(when) == time:
today = date.today()
now = datetime.now(tzutc()).timetz()
when = datetime.combine(today if now < when else today + timedelta(days=1), when)
elif type(when) == date:
when = datetime.combine(when, time(0, 0, tzinfo=tzutc()))
if delta and not when: # provide a period but no start
self.delta = delta
self.next = datetime.now(tzutc()) + delta
elif when and not delta: # provide a start but no period
self.delta = when - datetime.now(tzutc())
self.next = when
else: # provide a start and period, this should always be recurring
self.delta = delta
self.next = when
self.recurring = recurring
self.done = False
self.name = name
Hook.__init__(self, events.TASK, clean_args(action if action else identity))
logger.debug(self)
def get_subpop_ids(self, znodes, mnodes, pop_dict, linear_mass=1, lookback_time = False):
self.subpop_ids = {}
if lookback_time == True:
age_universe = cosmo.age(0).value # 13.797617455819209 Gyr
znodes = np.array([z_at_value(cosmo.age,(age_universe - i) * u.Gyr) for i in znodes])
for iz in range(len(znodes[:-1])):
for jm in range(len(mnodes[:-1])):
for k in pop_dict:
if linear_mass == 1:
ind_mz =( (self.table.sfg.values == pop_dict[k][0]) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(10**self.table[self.mkey] >= 10**np.min(mnodes[jm:jm+2])) & (10**self.table[self.mkey] < 10**np.max(mnodes[jm:jm+2])) )
else:
ind_mz =( (self.table.sfg == pop_dict[k][0]) & (self.table[self.zkey] >= np.min(znodes[iz:iz+2])) & (self.table[self.zkey] < np.max(znodes[iz:iz+2])) &
(self.table[self.mkey] >= np.min(mnodes[jm:jm+2])) & (self.table[self.mkey] < np.max(mnodes[jm:jm+2])) )
self.subpop_ids['z_'+clean_args(str('{:.2f}'.format(znodes[iz])))+'_'+clean_args(str('{:.2f}'.format(znodes[iz+1])))+'__m_'+clean_args(str('{:.2f}'.format(mnodes[jm])))+'_'+clean_args(str('{:.2f}'.format(mnodes[jm+1])))+'_'+k] = self.table.ID[ind_mz].values
def dissimilarities(methodname, listname, argsname=None, n_jobs=None, outdir=None):
if outdir == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
else:
if not os.path.exists(outdir):
tsh.makedirs(outdir)
inputname = os.path.splitext(os.path.basename(listname))[0]
if listname.endswith('.gz'):
inputname = os.path.splitext(inputname)[0]
meta, data = read_listfile(listname)
args = meta
if argsname != None:
args.update(read_argsfile(argsname))
args, w = compute_dissimilarity(methodname, args, data, n_jobs=n_jobs, output_dir=outdir, input_name=inputname)
if 'threshold' in args and args['threshold'] != 'False':
args, w = threshold_dissimilarity(args['threshold'], args, w)
dissim = prepare_weights_data(data['id'], data.dtype['id'], w)
clean_args(args)
write_listfile(os.path.join(outdir, inputname + '-dissim.csv.gz'), dissim, input_name=inputname, **args)
def propagate_predict(modelname, dissimname, predictionsname, outdir=None):
if outdir == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
else:
if not os.path.exists(outdir):
tsh.makedirs(outdir)
args = {}
predictions_meta, predictions = read_listfile(predictionsname)
args.update(predictions_meta)
dissim_meta, sample_ids, dissim = read_weightsfile(dissimname)
assert (predictions['id'] == np.array(sample_ids)).all()
assert predictions_meta['input_name'] == dissim_meta['input_name'], \
'Expecting same input names (%s x %s)' % (predictions_meta['input_name'], dissim_meta['input_name'])
inputname = predictions_meta['input_name']
args.update(dissim_meta)
model = read_propagatorfile(modelname)
args.update(model['meta'])
method_name = model['propagator']['method_name']
del model['propagator']['method_name']
args.update(model['propagator'])
args, prop = propagate(method_name, args, predictions, dissim, output_dir=outdir)
clean_args(args)
del args['cv_results']
write_listfile(os.path.join(outdir, inputname + '-propagated.csv.gz'), prop, **args)
def build_training_set(db,stacked_flux_densities, features_list, znodes, mnodes, knodes, Y_dict=None, k_init = 0, k_final = None, cc=0.5, ngal_cut=10):
nz = len(znodes)-1
nm = len(mnodes)-1
nk = len(knodes)
if k_final == None:
k_final = len(knodes)+1
training_set = {}
if Y_dict != None:
keys = [i for i in Y_dict.keys()]
key = keys[keys != 'Y_err']
training_set[key] = []
training_set['Y_err'] = []
for ft in features_list:
if ft in ['LMASS','lmass']:
training_set['stellar_mass'] = []
else:
training_set[ft] = []
for k in range(nk)[k_init:k_final]:
for im in range(nm):
mn = mnodes[im:im+2]
m_suf = '{:.2f}'.format(mn[0])+'-'+'{:.2f}'.format(mn[1])
for iz in range(nz):
zn = znodes[iz:iz+2]
z_suf = '{:.2f}'.format(zn[0])+'-'+'{:.2f}'.format(zn[1])
arg = clean_args('z_'+z_suf+'__m_'+m_suf+'_'+knodes[k])
ind = stacked_flux_densities.bin_ids[arg]
ngal = len(ind)
completeness_flag = completeness_flag_neural_net([np.mean(zn)],[np.mean(mn)],sfg=k, completeness_cut = cc)
if ((ngal > ngal_cut) & (completeness_flag == True)):
if Y_dict != None:
try:
training_set[key].append(Y_dict[key][arg][0])
except IndexError:
training_set[key].append(Y_dict[key][arg])
training_set['Y_err'].append(Y_dict['Y_err'][arg])
for ft in features_list:
if ft in['ltau','lage','a_hat_AGN','la2t']:
training_set[ft].append(10**subset_averages_from_ids(db.table,ind,ft))
elif ft in['LMASS','lmass']:
training_set['stellar_mass'].append(10**subset_averages_from_ids(db.table,ind,ft))
else:
training_set[ft].append(subset_averages_from_ids(db.table,ind,ft))
return training_set
def measure_cib(stacked_object, area_deg=1.62, tcib=False):
'''
Sums the contribution from sources (in each bin) to the CIB at each wavelength.
If tcib == True, output is sum of all bins at each wavelength.
'''
if area_deg == 1.62:
print 'defaulting to uVista/COSMOS area of 1.62deg2'
area_sr = area_deg * (3.1415926535 / 180.)**2
cib = np.zeros(np.shape(stacked_object.simstack_nuInu_array))
for iwv in range(stacked_object.nw):
for i in range(stacked_object.nz):
zn = stacked_object.z_nodes[i:i+2]
z_suf = '{:.2f}'.format(zn[0])+'-'+'{:.2f}'.format(zn[1])
for j in range(stacked_object.nm):
mn = stacked_object.m_nodes[j:j+2]
m_suf = '{:.2f}'.format(mn[0])+'-'+'{:.2f}'.format(mn[1])
for p in range(stacked_object.npops):
arg = clean_args('z_'+z_suf+'__m_'+m_suf+'_'+stacked_object.pops[p])
ng = len(stacked_object.bin_ids[arg])
cib[iwv,i,j,p] += 1e-9 * float(ng) / area_sr * stacked_object.simstack_nuInu_array[iwv,i,j,p]
if tcib == True:
return np.sum(np.sum(np.sum(cib,axis=1),axis=1),axis=1)
else:
return cib
parser = argparse.ArgumentParser(description='Computes features for all the input data.')
parser.add_argument('-c', '--config', dest='config', required=False, action='store', default=None, help='Path to the config file')
parser.add_argument('-m', '--method', dest='method', required=True, action='store', choices=method_table.keys(), default=None, help='Method name.')
parser.add_argument('-a', '--args', dest='args', required=False, action='store', default=None, help='Method arguments file.')
parser.add_argument('-l', '--list', dest='list', required=True, action='store', default=None, help='List file.')
parser.add_argument('-j', '--jobs', dest='jobs', required=False, action='store', default=None, type=int, help='Number of parallel processes.')
parser.add_argument('-o', '--output', dest='output', required=False, action='store', default=None, help='Output directory.')
opts = parser.parse_args()
if opts.output == None:
outdir = tempfile.mkdtemp(dir=os.curdir, prefix='out')
logger.info('Output directory %s', outdir)
else:
outdir = opts.output
if not os.path.exists(outdir):
tsh.makedirs(outdir)
inputname = os.path.splitext(os.path.basename(opts.list))[0]
if opts.list.endswith('.gz'):
inputname = os.path.splitext(inputname)[0]
outputname = os.path.join(outdir, inputname + '-feats.csv.gz')
if os.path.exists(outputname):
logger.info('Skipping file %s, already exists.', outputname)
else:
config = tsh.read_config(opts, __file__)
meta, data = read_listfile(opts.list)
args = meta
if opts.args != None:
args.update(read_argsfile(opts.args))
args, features = compute_features(opts.method, args, data, input_name=inputname, n_jobs=opts.jobs, output_dir=outdir)
clean_args(args)
write_listfile(outputname, features, input_name=inputname, **args)
parser.add_argument('-a',
'--args',
dest='args',
required=True,
action='store',
default=None,
help='Method arguments file.')
parser.add_argument('--random-seed',
dest='seed',
required=False,
action='store',
type=int,
default=-1,
help='Random seed, by default use time.')
parser.add_argument('output',
action='store',
default=None,
help='Output file.')
opts = parser.parse_args()
config = tsh.read_config(opts, __file__)
if opts.seed == -1:
seed = int(time.time() * 1024 * 1024 + time.time())
else:
seed = opts.seed
np.random.seed(seed)
args = read_argsfile(opts.args)
args, data = generate(**args)
args['random_seed'] = seed
clean_args(args)
write_listfile(opts.output, data, **args)
def read_pickles(self):
if self.params['bootstrap'] == True:
print('creating bootstrap array w/ size '+str(self.nw)+'bands; '+str(self.nz)+'redshifts; '+str(self.nm)+'masses; '+str(self.npops)+'populations; '+str(self.nboots)+' bootstraps')
bootstrap_fluxes = np.zeros([self.nw,self.nz,self.nm,self.npops,self.nboots])
bootstrap_errors = np.zeros([self.nw,self.nz,self.nm,self.npops,self.nboots])
bootstrap_intensities = np.zeros([self.nw,self.nz,self.nm,self.npops,self.nboots])
else:
print('creating simstack array w/ size '+str(self.nw)+'bands; '+str(self.nz)+'redshifts; '+str(self.nm)+'masses; '+str(self.npops)+'populations')
stacked_fluxes = np.zeros([self.nw,self.nz,self.nm,self.npops])
stacked_errors = np.zeros([self.nw,self.nz,self.nm,self.npops])
stacked_intensities = np.zeros([self.nw,self.nz,self.nm,self.npops])
if self.params['bins']['bin_in_lookback_time'] == True:
ndec = 2
else:
ndec = 1
slice_keys = self.slice_key_builder(ndecimal=ndec)
#pdb.set_trace()
for i in range(self.nz):
z_slice = slice_keys[i]
z_suf = 'z_'+ self.z_keys[i]
if self.params['bootstrap'] == True:
for k in np.arange(self.nboots) + int(self.params['boot0']):
if self.params['bins']['stack_all_z_at_once'] == True:
filename_boots = 'simstack_flux_densities_'+ self.params['io']['shortname'] + '_all_z' + '_boot_'+ str(k) + '.p'
else:
filename_boots = 'simstack_flux_densities_'+ self.params['io']['shortname'] + '_' + z_slice + '_boot_'+ str(k) + '.p'
if os.path.exists(self.path+filename_boots):
bootstack = pickle.load( open( self.path + filename_boots, "rb" ))
if self.params['save_bin_ids'] == True:
for bbk in bootstack[0].keys():
self.bin_ids[bbk+'_'+str(k)] = bootstack[0][bbk]
for wv in range(self.nw):
#pdb.set_trace1()
if self.params['save_bin_ids'] == True:
try:
single_wv_stacks = bootstack[1][z_slice][self.maps[wv]]
except:
single_wv_stacks = bootstack[1][self.maps[wv]]
else:
try:
single_wv_stacks = bootstack[z_slice][self.maps[wv]]
except:
single_wv_stacks = bootstack[self.maps[wv]]
for j in range(self.nm):
m_suf = 'm_' + self.m_keys[j]
for p in range(self.npops):
p_suf = self.pops[p]
key = clean_args(z_suf+'__'+ m_suf+ '_' + p_suf)
#pdb.set_trace()
try:
bootstrap_fluxes[wv,i,j,p,k] = single_wv_stacks[key].value
bootstrap_errors[wv,i,j,p,k] = single_wv_stacks[key].stderr
bootstrap_intensities[wv,i,j,p,k] = single_wv_stacks[key].value * (self.fqs[wv]) * 1e-26 * 1e9
except:
bootstrap_fluxes[wv,i,j,p,k] = single_wv_stacks[key]['value']
bootstrap_errors[wv,i,j,p,k] = single_wv_stacks[key]['stderr']
bootstrap_intensities[wv,i,j,p,k] = single_wv_stacks[key]['value'] * (self.fqs[wv]) * 1e-26 * 1e9
self.bootstrap_flux_array = bootstrap_fluxes
self.bootstrap_error_array = bootstrap_errors
self.bootstrap_nuInu_array = bootstrap_intensities
else:
if self.params['bins']['stack_all_z_at_once'] == True:
filename_stacks = 'simstack_flux_densities_'+ self.params['io']['shortname'] + '_all_z' + '.p'
else:
filename_stacks = 'simstack_flux_densities_'+ self.params['io']['shortname'] + '_' + z_slice + '.p'
if os.path.exists(self.path+filename_stacks):
simstack = pickle.load( open( self.path + filename_stacks, "rb" ))
#pdb.set_trace()
for ssk in simstack[0]:
self.bin_ids[ssk] = simstack[0][ssk]
for wv in range(self.nw):
try:
single_wv_stacks = simstack[1][z_slice][self.maps[wv]]
except:
single_wv_stacks = simstack[1][self.maps[wv]]
for j in range(self.nm):
m_suf = 'm_' + self.m_keys[j]
for p in range(self.npops):
p_suf = self.pops[p]
key = clean_args(z_suf+'__'+ m_suf+ '_' + p_suf)
try:
stacked_fluxes[wv,i,j,p] = single_wv_stacks[key].value
try:
stacked_errors[wv,i,j,p] = single_wv_stacks[key].psnerr
except:
stacked_errors[wv,i,j,p] = single_wv_stacks[key].stderr
stacked_intensities[wv,i,j,p] = single_wv_stacks[key].value * (self.fqs[wv]*1e9) * 1e-26 * 1e9
except:
stacked_fluxes[wv,i,j,p] = single_wv_stacks[key]['value']
try:
stacked_errors[wv,i,j,p] = single_wv_stacks[key]['psnerr']
except:
stacked_errors[wv,i,j,p] = single_wv_stacks[key]['stderr']
stacked_intensities[wv,i,j,p] = single_wv_stacks[key]['value'] * (self.fqs[wv]*1e9) * 1e-26 * 1e9
self.simstack_flux_array = stacked_fluxes
self.simstack_error_array = stacked_errors
self.simstack_nuInu_array = stacked_intensities
def stack_libraries_in_layers_w_background(
map_library,
subcatalog_library,
quiet=None):
print 'stacking with floating background'
map_names = [i for i in map_library.keys()]
# All wavelengths in cwavelengths
cwavelengths = [map_library[i].wavelength for i in map_names]
# Unique wavelengths in uwavelengths
uwavelengths = np.sort(np.unique(cwavelengths))
# nwv the number of unique wavelengths
nwv = len(uwavelengths)
lists = subcatalog_library.keys()
nlists = len(lists)
stacked_layers = {}
cwavelengths = []
radius = 1.1
for iwv in range(nwv):
print 'stacking '+map_library.keys()[iwv]
#READ MAPS
cmap = map_library[map_library.keys()[iwv]].map
cnoise = map_library[map_library.keys()[iwv]].noise
cwv = map_library[map_library.keys()[iwv]].wavelength
cname = map_library.keys()[iwv]
cwavelengths.append(cwv)
chd = map_library[map_library.keys()[iwv]].header
pixsize = map_library[map_library.keys()[iwv]].pixel_size
kern = map_library[map_library.keys()[iwv]].psf
fwhm = map_library[map_library.keys()[iwv]].fwhm
cw = WCS(chd)
cms = np.shape(cmap)
zeromask = np.ones(np.shape(cmap))
#ind_map_zero = np.where(np.isnan(cmap))
ind_map_zero = np.where(clean_nans(cmap) == 0.0)
zeromask[ind_map_zero] = 0.0
#pdb.set_trace()
# STEP 1 - Make Layers Cube at each wavelength
layers=np.zeros([nlists+1,cms[0],cms[1]])
ngals_layer = {}
for k in range(nlists):
s = lists[k]
if len(subcatalog_library[s][0]) > 0:
ra = subcatalog_library[s][0]
dec = subcatalog_library[s][1]
ty,tx = cw.wcs_world2pix(ra, dec, 0)
# CHECK FOR SOURCES THAT FALL OUTSIDE MAP
ind_keep = np.where((np.round(tx) >= 0) & (np.round(tx) < cms[0]) & (np.round(ty) >= 0) & (np.round(ty) < cms[1]))
real_x=np.round(tx[ind_keep]).astype(int)
real_y=np.round(ty[ind_keep]).astype(int)
# CHECK FOR SOURCES THAT FALL ON ZEROS
ind_nz=np.where(cmap[real_x,real_y] != 0 )
nt = np.shape(ind_nz)[1]
ngals_layer[s] = nt
#print 'ngals: ' + str(nt)
if nt > 0:
real_x = real_x[ind_nz]
real_y = real_y[ind_nz]
for ni in range(nt):
layers[k, real_x[ni],real_y[ni]]+=1.0
else: ngals_layer[s] = 1
# STEP 2 - Convolve Layers and put in pixels
flattened_pixmap = np.sum(layers,axis=0)
total_circles_mask = circle_mask(flattened_pixmap, radius * fwhm, pixsize)
#ind_fit = np.where(total_circles_mask >= 1)
ind_fit = np.where((total_circles_mask >= 1) & (zeromask != 0))
del total_circles_mask
nhits = np.shape(ind_fit)[1]
###
cfits_flat = np.asarray([])
cfits_flat = np.append(cfits_flat,np.ndarray.flatten(np.ones(len(ind_fit))))
###
#pdb.set_trace()
for u in range(nlists):
layer = layers[u,:,:]
tmap = smooth_psf(layer, kern)
cfits_flat = np.append(cfits_flat,np.ndarray.flatten(tmap[ind_fit]))
cmap[ind_fit] -= np.mean(cmap[ind_fit], dtype=np.float32)
imap = np.ndarray.flatten(cmap[ind_fit])
ierr = np.ndarray.flatten(cnoise[ind_fit])
fit_params = Parameters()
fit_params.add('cib_background',value=1e-5*np.random.randn())
for iarg in range(nlists):
arg = clean_args(lists[iarg])
fit_params.add(arg,value= 1e-3*np.random.randn())
if len(ierr)==0: pdb.set_trace()
cov_ss_1d = minimize(simultaneous_stack_array_oned, fit_params,
args=(cfits_flat,), kws={'data1d':imap,'err1d':ierr}, nan_policy = 'propagate')
del cfits_flat, imap, ierr
#Dictionary keys decided here. Was originally wavelengths. Changing it back to map_names
packed_fluxes = pack_fluxes(cov_ss_1d.params)
packed_stn = pack_simple_poisson_errors(cov_ss_1d.params,ngals_layer,crms)
stacked_layers[cname] = packed_stn # packed_fluxes
gc.collect
return stacked_layers
def get_parent_child_redshift_bins(self,znodes):
self.id_z_sed = {}
for ch in self.table.parent.unique():
for iz in range(len(znodes[:-1])):
self.id_z_sed['z_'+clean_args(str(znodes[iz]))+'_'+clean_args(str(znodes[iz+1]))+'__sed'+str(ch)] = self.table.ID[ (self.table.parent == ch) & (self.table[self.zkey] >= znodes[iz]) & (self.table[self.zkey] < znodes[iz+1]) ].values
def decorated(function):
function = Hook(events.TEARDOWN, clean_args(function))
self._hooks[events.TEARDOWN].insert(
0 if priority else len(self._hooks[events.SETUP]), function)
return function