def __init__(self, z=0, t0=0, x0=1, x1=0, c=0, snra=0, sndec=0):
"""
Parameters
----------
z: float [0]
Redshift of the SNIa object to pass to sncosmo.
t0: float [0]
Time in mjd of phase=0, corresponding to the B-band
maximum.
x0: float [1]
Normalization factor for the lightcurves.
x1: float [0]
Empirical parameter controlling the stretch in time of the
light curves
c: float [0]
Empirical parameter controlling the colors.
snra: float [0]
RA in degrees of the SNIa.
sndec: float [0]
Dec in degrees of the SNIa.
"""
self.sn_obj = SNObject(snra, sndec)
self.sn_obj.set(z=z,
t0=t0,
x0=x0,
x1=x1,
c=c,
hostebv=0,
hostr_v=3.1,
mwebv=0,
mwr_v=3.1)
self.bp_dict = self.lsst_bp_dict
def astro_object(self, idValue, mjdOffset=59580.):
"""
instance of the catsim representation of the astrophysical object.
Parameters
----------
idValue : int, mandatory
index of the astro_object
mjdOffset : float, optional, defaults to 59580.
offset in time parameters in the database for the transient objects
Returns
-------
Instance of astro_object with parameters from the database
Examples
--------
>>> sn = reflc.astro_object(idValue=6001163623700)
"""
df = self.get_params(idValue)
sn = SNObject(ra=df.snra.values[0], dec=df.sndec.values[0])
paramDict = dict()
for param in ['t0', 'x0', 'x1', 'c']:
paramDict[param] = df[param].values
paramDict['t0'] += mjdOffset
paramDict['z'] = df.redshift.values[0]
sn.set(**paramDict)
return sn
def SNobj(fieldID, t0, snState=None, peakAbsMagBesselB=-19.3):
sn = SNObject(ra=np.degrees(so.ra(fieldID)),
dec=np.degrees(so.dec(fieldID)))
sn.set(t0=t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(peakAbsMagBesselB, 'bessellB', 'ab')
return sn
def lc(self, idx, maxObsHistID=None):
"""
Parameters
----------
"""
if maxObsHistID is None:
maxObsHistID = self.maxObsHistID
# obtain the model parameters from the population
paramDict = self.population.modelparams(idx)
self.model.setModelParameters(**paramDict)
myra = paramDict['ra']
mydec = paramDict['dec']
timeRange = (self.model.minMjd, self.model.maxMjd)
if None not in timeRange:
queryTime = 'expMJD < {1} and expMJD > {0}'.format(timeRange[0], timeRange[1])
df = self.pointings.copy().query(queryTime)
else:
df = self.pointings.copy()
if self.pruneWithRadius:
raise ValueError('Not implemented')
numObs = len(self.pointings)
modelFlux = np.zeros(numObs)
fluxerr = np.zeros(numObs)
sn = SNObject(myra, mydec)
for i, rowtuple in enumerate(df.iterrows()):
row = rowtuple[1]
# print(row['expMJD'], row['filter'], row['fiveSigmaDepth'])
bp = self.bandPasses[row['filter']]
modelFlux[i] = self.model.modelFlux(row['expMJD'],
bandpassobj=bp)
fluxerr[i] = sn.catsimBandFluxError(time=row['expMJD'],
bandpassobject=bp,
fluxinMaggies=modelFlux[i],
m5=row['fiveSigmaDepth'])
rng = self.randomState
df.reset_index(inplace=True)
df['objid'] = np.ones(numObs)*np.int(idx)
df['objid'] = df.objid.astype(np.int)
df['fluxerr'] = fluxerr
deviations = rng.normal(size=len(df))
df['deviations'] = deviations
df['zp'] = 0.
df['ModelFlux'] = modelFlux
df['flux'] = df['ModelFlux'] + df['deviations'] * df['fluxerr']
df['zpsys']= 'ab'
df['pid'] = self.pair_method(df.objid, df.obsHistID, self.maxObsHistID)
df['pid'] = df.pid.astype(np.int)
lc = df[['pid', 'obsHistID', 'objid', 'expMJD', 'filter', 'ModelFlux', 'fieldID', 'flux',
'fluxerr', 'deviations', 'zp', 'zpsys']]
lc.set_index('pid', inplace=True)
return lc
def load_SNsed(self):
"""
returns a list of SN seds in `lsst.sims.photUtils.Sed` observed within
the spatio-temporal range specified by obs_metadata
"""
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
SNobject = SNObject()
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
sedlist = []
for i in range(self.numobjs):
SNobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
SNobject.setCoords(ra=raDeg[i], dec=decDeg[i])
SNobject.mwEBVfromMaps()
sed = SNobject.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandpassDict,
applyExitinction=True)
sedlist.append(sed)
return sedlist
def test_attributeDefaults(self):
"""
Check the defaults and the setter properties for rectifySED and
modelOutSideRange
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
self.assertEqual(snobj.rectifySED, True)
self.assertEqual(snobj.modelOutSideTemporalRange, 'zero')
snobj.rectifySED = False
self.assertFalse(snobj.rectifySED, False)
self.assertEqual(snobj.modelOutSideTemporalRange, 'zero')
def test_raisingerror_forunimplementedmodelOutSideRange(self):
"""
check that correct error is raised if the user tries to assign an
un-implemented model value to
`sims.catUtils.supernovae.SNObject.modelOutSideTemporalRange`
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
assert snobj.modelOutSideTemporalRange == 'zero'
with self.assertRaises(ValueError) as context:
snobj.modelOutSideTemporalRange = 'False'
self.assertEqual('Model not implemented, defaulting to zero method\n',
context.exception.args[0])
def calc_sne_mags(self, obs_mjd, obs_filter):
wavelen_max = 1800.
wavelen_min = 30.
wavelen_step = 0.1
sn_magnorm_list = []
sn_sed_names = []
add_to_cat_list = []
for idx in range(len(self.truth_cat)):
sed_mjd = obs_mjd - self.truth_cat['t_delay'].iloc[idx]
current_sn_obj = SNObject(ra=self.truth_cat['ra'].iloc[idx],
dec=self.truth_cat['dec'].iloc[idx])
current_sn_obj.set(z=self.truth_cat['redshift'].iloc[idx],
t0=self.truth_cat['t0'].iloc[idx],
x0=self.truth_cat['x0'].iloc[idx],
x1=self.truth_cat['x1'].iloc[idx],
c=self.truth_cat['c'].iloc[idx])
# Following follows from
# https://github.com/lsst/sims_catUtils/blob/master/python/lsst/sims/catUtils/mixins/sncat.py
sn_sed_obj = current_sn_obj.SNObjectSourceSED(
time=sed_mjd,
wavelen=np.arange(wavelen_min, wavelen_max, wavelen_step))
flux_500 = sn_sed_obj.flambda[np.where(
sn_sed_obj.wavelen >= 499.99)][0]
if flux_500 > 0.:
sn_magnorm = sn_sed_obj.calcMag(bandpass=self.imSimBand)
sn_name = None
if self.write_sn_sed:
sn_name = '%s/specFileGLSN_%s_%s_%.4f.txt' % (
self.sed_folder_name,
self.truth_cat['dc2_sys_id'].iloc[idx],
self.truth_cat['image_number'].iloc[idx], obs_mjd)
sed_filename = '%s/%s' % (self.out_dir, sn_name)
sn_sed_obj.writeSED(sed_filename)
with open(sed_filename, 'rb') as f_in, gzip.open(
str(sed_filename + '.gz'), 'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
os.remove(sed_filename)
sn_magnorm_list.append(sn_magnorm)
sn_sed_names.append(sn_name + '.gz')
add_to_cat_list.append(idx)
return add_to_cat_list, np.array(sn_magnorm_list), sn_sed_names
def test_rectifiedSED(self):
"""
Check for an extreme case that the SN seds are being rectified. This is
done by setting up an extreme case where there will be negative seds, and
checking that this is indeed the case, and checking that they are not
negative if rectified.
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
snobj.set(z=0.96, t0=self.mjdobs, x1=-3., x0=1.8e-6)
snobj.rectifySED = False
times = np.arange(self.mjdobs - 50., self.mjdobs + 150., 1.)
badTimes = []
for time in times:
sed = snobj.SNObjectSED(time=time,
bandpass=self.lsstBandPass['r'])
if any(sed.flambda < 0.):
badTimes.append(time)
# Check that there are negative SEDs
assert(len(badTimes) > 0)
snobj.rectifySED = True
for time in badTimes:
sed = snobj.SNObjectSED(time=time,
bandpass=self.lsstBandPass['r'])
self.assertGreaterEqual(sed.calcADU(bandpass=self.lsstBandPass['r'],
photParams=self.rectify_photParams), 0.)
self.assertFalse(any(sed.flambda < 0.))
def get_phosimVars(self):
"""
Obtain variables sedFilepath to be used to obtain unique filenames
for each SED for phoSim and MagNorm which is also used. Note that aside
from acting as a getter, this also writes spectra to
`self.sn_sedfile_prefix`snid_mjd_band.dat for each observation of
interest
"""
# construct the unique filename
# method: snid_mjd(to 4 places of decimal)_bandpassname
mjd = "_{:0.4f}_".format(self.mjdobs)
mjd += self.obs_metadata.bandpass + '.dat'
fnames = np.array([
self.sn_sedfile_prefix + str(int(elem)) + mjd if isinstance(
elem, numbers.Number) else self.sn_sedfile_prefix + str(elem) +
mjd for elem in self.column_by_name('snid')
],
dtype='str')
c, x1, x0, t0, z = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift')
bp = Bandpass()
bp.imsimBandpass()
magNorms = np.zeros(len(fnames))
snobject = SNObject()
snobject.rectifySED = True
for i in range(len(self.column_by_name('snid'))):
# if t0 is nan, this was set by the catalog for dim SN, or SN
# outside redshift range, We will not provide a SED file for these
if np.isnan(t0[i]):
magNorms[i] = np.nan
fnames[i] = None
else:
snobject.set(c=c[i], x1=x1[i], x0=x0[i], t0=t0[i], z=z[i])
if snobject.modelOutSideTemporalRange == 'zero':
if self.mjdobs > snobject.maxtime(
) or self.mjdobs < snobject.mintime():
magNorms[i] = np.nan
fnames[i] = None
# SED in rest frame
sed = snobject.SNObjectSourceSED(time=self.mjdobs)
try:
magNorms[i] = sed.calcMag(bandpass=bp)
except:
# sed.flambda = 1.0e-20
magNorms[i] = 1000. # sed.calcMag(bandpass=bp)
if self.writeSedFile:
sed.writeSED(fnames[i])
return (fnames, magNorms)
def load_SNsed(self):
"""
returns a list of SN seds in `lsst.sims.photUtils.Sed` observed within
the spatio-temporal range specified by obs_metadata
"""
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
SNobject = SNObject()
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
sedlist = []
for i in range(self.numobjs):
SNobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
SNobject.setCoords(ra=raDeg[i], dec=decDeg[i])
SNobject.mwEBVfromMaps()
sed = SNobject.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandpassDict,
applyExitinction=True)
sedlist.append(sed)
return sedlist
def SN(self):
"""
`lsst.sims.catsim.SNObject` instance with peakMJD set to t0
"""
if self.snState is not None:
return SNObject.fromSNState(self.snState)
sn = SNObject(ra=self.radeg, dec=self.decdeg)
sn.set(t0=self.t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(self.bessellBpeakabsmag, 'bessellB', 'ab')
return sn
def SNobj(fieldID, t0, snState=None):
sn = SNObject(ra=np.degrees(so.ra(fieldID)),
dec=np.degrees(so.dec(fieldID)))
sn.set(t0=t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(bessellBpeakabsmag, 'bessellB', 'ab')
return sn
def setUp(self):
"""
Setup tests
SN_blank: A SNObject with no MW extinction
"""
mydir = get_config_dir()
print('===============================')
print('===============================')
print(mydir)
print('===============================')
print('===============================')
# A range of wavelengths in Ang
self.wave = np.arange(3000., 12000., 50.)
# Equivalent wavelenths in nm
self.wavenm = self.wave / 10.
# Time to be used as Peak
self.mjdobs = 571190
# Check that we can set up a SED
# with no extinction
self.SN_blank = SNObject()
self.SN_blank.setCoords(ra=30., dec=-60.)
self.SN_blank.set(z=0.96, t0=571181, x1=2.66, c=0.353, x0=1.796e-6)
self.SN_blank.set_MWebv(0.)
self.SN_extincted = SNObject(ra=30., dec=-60.)
self.SN_extincted.set(z=0.96,
t0=571181,
x1=2.66,
c=0.353,
x0=1.796112e-06)
self.SNCosmoModel = self.SN_extincted.equivalentSNCosmoModel()
self.rectify_photParams = PhotometricParameters()
self.lsstBandPass = BandpassDict.loadTotalBandpassesFromFiles()
self.SNCosmoBP = sncosmo.Bandpass(wave=self.lsstBandPass['r'].wavelen,
trans=self.lsstBandPass['r'].sb,
wave_unit=astropy.units.Unit('nm'),
name='lsst_r')
def setUp(self):
"""
Setup tests
SN_blank: A SNObject with no MW extinction
"""
from astropy.config import get_config_dir
mydir = get_config_dir()
print '==============================='
print '==============================='
print (mydir)
print '==============================='
print '==============================='
# A range of wavelengths in Ang
self.wave = np.arange(3000., 12000., 50.)
# Equivalent wavelenths in nm
self.wavenm = self.wave / 10.
# Time to be used as Peak
self.mjdobs = 571190
# Check that we can set up a SED
# with no extinction
self.SN_blank = SNObject()
self.SN_blank.setCoords(ra=30., dec=-60.)
self.SN_blank.set(z=0.96, t0=571181, x1=2.66, c=0.353, x0=1.796e-6)
self.SN_blank.set_MWebv(0.)
self.SN_extincted = SNObject(ra=30., dec=-60.)
self.SN_extincted.set(z=0.96, t0=571181, x1=2.66, c=0.353,
x0=1.796112e-06)
self.SNCosmoModel = self.SN_extincted.equivalentSNCosmoModel()
self.lsstBandPass = BandpassDict.loadTotalBandpassesFromFiles()
self.SNCosmoBP = sncosmo.Bandpass(wave=self.lsstBandPass['r'].wavelen,
trans=self.lsstBandPass['r'].sb,
wave_unit=astropy.units.Unit('nm'),
name='lsst_r')
def SN(self):
"""
`lsst.sims.catsim.SNObject` instance with peakMJD set to t0
"""
if self.snState is not None:
return SNObject.fromSNState(self.snState)
sn = SNObject(ra=self.radeg, dec=self.decdeg)
sn.set(t0=self.t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(self.bessellBpeakabsmag, 'bessellB', 'ab')
return sn
def get_snfluxes(self):
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
snobject = SNObject()
# Initialize return array
vals = np.zeros(shape=(self.numobjs, 19))
for i, _ in enumerate(vals):
snobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
snobject.setCoords(ra=raDeg[i], dec=decDeg[i])
snobject.mwEBVfromMaps()
# Calculate fluxes
vals[i, :6] = snobject.catsimManyBandFluxes(time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
observedBandPassInd=None)
# Calculate magnitudes
vals[i, 6:12] = snobject.catsimManyBandMags(time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
observedBandPassInd=None)
vals[i, 12:18] = snobject.catsimManyBandADUs(time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
photParams=self.photometricparameters)
vals[i, 18] = snobject.ebvofMW
return (vals[:, 0], vals[:, 1], vals[:, 2], vals[:, 3],
vals[:, 4], vals[:, 5], vals[:, 6], vals[:, 7],
vals[:, 8], vals[:, 9], vals[:, 10], vals[:, 11],
vals[:, 12], vals[:, 13], vals[:, 14], vals[:, 15],
vals[:, 16], vals[:, 17], vals[:, 18])
def SN(self):
"""
`lsst.sims.catsim.SNObject` instance with peakMJD set to t0
"""
if self._SN is not None:
pass
# return self._SN
elif self.snState is not None:
self._SN = SNObject.fromSNState(self.snState)
else:
sn = SNObject(ra=self.radeg, dec=self.decdeg)
sn.set(t0=self.t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(self.peakAbsMagBesselB, 'bessellB', 'ab')
self._SN = sn
return self._SN
def get_phosimVars(self):
"""
Obtain variables sedFilepath to be used to obtain unique filenames
for each SED for phoSim and MagNorm which is also used. Note that aside
from acting as a getter, this also writes spectra to
`self.sn_sedfile_prefix`snid_mjd_band.dat for each observation of
interest
"""
# construct the unique filename
# method: snid_mjd(to 4 places of decimal)_bandpassname
mjd = "_{:0.4f}_".format(self.mjdobs)
mjd += self.obs_metadata.bandpass + '.dat'
fnames = np.array([self.sn_sedfile_prefix + str(int(elem)) + mjd
if isinstance(elem, numbers.Number) else
self.sn_sedfile_prefix + str(elem) + mjd
for elem in self.column_by_name('snid')], dtype='str')
c, x1, x0, t0, z = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift')
bp = Bandpass()
bp.imsimBandpass()
magNorms = np.zeros(len(fnames))
snobject = SNObject()
snobject.rectifySED = True
for i in range(len(self.column_by_name('snid'))):
# if t0 is nan, this was set by the catalog for dim SN, or SN
# outside redshift range, We will not provide a SED file for these
if np.isnan(t0[i]):
magNorms[i] = np.nan
fnames[i] = None
else:
snobject.set(c=c[i], x1=x1[i], x0=x0[i], t0=t0[i],
z=z[i])
if snobject.modelOutSideTemporalRange == 'zero':
if self.mjdobs > snobject.maxtime() or self.mjdobs < snobject.mintime():
magNorms[i] = np.nan
fnames[i] = None
# SED in rest frame
sed = snobject.SNObjectSourceSED(time=self.mjdobs)
try:
magNorms[i] = sed.calcMag(bandpass=bp)
except:
# sed.flambda = 1.0e-20
magNorms[i] = 1000. # sed.calcMag(bandpass=bp)
if self.writeSedFile:
sed.writeSED(fnames[i])
return (fnames, magNorms)
def SN(self):
"""
`lsst.sims.catsim.SNObject` instance with peakMJD set to t0
"""
if self._SN is not None:
pass
# return self._SN
elif self.snState is not None:
self._SN = SNObject.fromSNState(self.snState)
else :
sn = SNObject(ra=self.radeg, dec=self.decdeg)
sn.set(t0=self.t0)
sn.set(z=0.5)
sn.set_source_peakabsmag(self.peakAbsMagBesselB, 'bessellB', 'ab')
self._SN = sn
return self._SN
def getSNCosmomags(mjd, filt, snpars_table, snid_in='MS_9940_3541'):
asn = snpars_table.loc[snpars_table['snid_in'] == snid_in]
sn_mod = SNObject(ra=asn.snra_in[0], dec=asn.sndec_in[0])
sn_mod.set(z=asn.z_in[0],
t0=asn.t0_in[0],
x1=asn.x1_in[0],
c=asn.c_in[0],
x0=asn.x0_in[0])
# this is probably not the thing to do
flux = sn_mod.catsimBandFlux(mjd, LSST_BPass[filt])
mag = sn_mod.catsimBandMag(LSST_BPass[filt], mjd, flux)
return (flux, mag)
def _calculate_batch_of_sn(self, sn_truth_params, mjd_arr, filter_arr,
out_dict, tag):
"""
For processing SNe in batches using multiprocessing
-----
sn_truth_params is a numpy array of json-ized
dicts defining the state of an SNObject
mjd_arr is a numpy array of the TAI times of
observations
filter_arr is a numpy array of ints indicating
the filter being observed at each time
out_dict is a multprocessing.Manager().dict() to store
the results
tag is an integer denoting which batch of SNe this is.
"""
int_to_filter = 'ugrizy'
mags = np.NaN*np.ones((len(sn_truth_params), len(mjd_arr)), dtype=float)
for i_obj, sn_par in enumerate(sn_truth_params):
sn_obj = SNObject.fromSNState(json.loads(sn_par))
for i_time in range(len(mjd_arr)):
mjd = mjd_arr[i_time]
filter_name = int_to_filter[filter_arr[i_time]]
if mjd < sn_obj.mintime() or mjd > sn_obj.maxtime():
continue
bp = self._bp_dict[filter_name]
sn_sed = sn_obj.SNObjectSED(mjd, bandpass=bp,
applyExtinction=False)
ff = sn_sed.calcFlux(bp)
if ff>1.0e-300:
mm = sn_sed.magFromFlux(ff)
mags[i_obj][i_time] = mm
out_dict[tag] = mags
def get_snbrightness(self):
"""
getters for brightness related parameters of sn
"""
if self._sn_object_cache is None or len(self._sn_object_cache) > 1000000:
self._sn_object_cache = {}
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
ebv = self.column_by_name('EBV')
id_list = self.column_by_name('snid')
bandname = self.obs_metadata.bandpass
if isinstance(bandname, list):
raise ValueError('bandname expected to be string, but is list\n')
bandpass = self.lsstBandpassDict[bandname]
# Initialize return array so that it contains the values you would get
# if you passed through a t0=self.badvalues supernova
vals = np.array([[0.0]*len(t0), [np.inf]*len(t0),
[np.nan]*len(t0), [np.inf]*len(t0),
[0.0]*len(t0)]).transpose()
for i in np.where(np.logical_and(np.isfinite(t0),
np.abs(self.mjdobs - t0) < self.maxTimeSNVisible))[0]:
if id_list[i] in self._sn_object_cache:
SNobject = self._sn_object_cache[id_list[i]]
else:
SNobject = SNObject()
SNobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
SNobject.setCoords(ra=raDeg[i], dec=decDeg[i])
SNobject.set_MWebv(ebv[i])
self._sn_object_cache[id_list[i]] = SNobject
if self.mjdobs <= SNobject.maxtime() and self.mjdobs >= SNobject.mintime():
# Calculate fluxes
fluxinMaggies = SNobject.catsimBandFlux(time=self.mjdobs,
bandpassobject=bandpass)
mag = SNobject.catsimBandMag(time=self.mjdobs,
fluxinMaggies=fluxinMaggies,
bandpassobject=bandpass)
vals[i, 0] = fluxinMaggies
vals[i, 1] = mag
flux_err = SNobject.catsimBandFluxError(time=self.mjdobs,
bandpassobject=bandpass,
m5=self.obs_metadata.m5[
bandname],
photParams=self.photometricparameters,
fluxinMaggies=fluxinMaggies,
magnitude=mag)
mag_err = SNobject.catsimBandMagError(time=self.mjdobs,
bandpassobject=bandpass,
m5=self.obs_metadata.m5[
bandname],
photParams=self.photometricparameters,
magnitude=mag)
sed = SNobject.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandpassDict,
applyExtinction=True)
adu = sed.calcADU(bandpass, photParams=self.photometricparameters)
vals[i, 2] = flux_err
vals[i, 3] = mag_err
vals[i, 4] = adu
return (vals[:, 0], vals[:, 1], vals[:, 2], vals[:, 3], vals[:, 4])
def __init__(self,
catsim_cat,
visit_mjd,
specFileMap,
sed_path,
om10_cat='twinkles_lenses_v2.fits',
sne_cat='dc2_sne_cat.csv',
density_param=1.,
cached_sprinkling=False,
agn_cache_file=None,
sne_cache_file=None,
defs_file=None):
"""
Parameters
----------
catsim_cat: catsim catalog
The results array from an instance catalog.
visit_mjd: float
The mjd of the visit
specFileMap:
This will tell the instance catalog where to write the files
om10_cat: optional, defaults to 'twinkles_lenses_v2.fits
fits file with OM10 catalog
sne_cat: optional, defaults to 'dc2_sne_cat.csv'
density_param: `np.float`, optioanl, defaults to 1.0
the fraction of eligible agn objects that become lensed and should
be between 0.0 and 1.0.
cached_sprinkling: boolean
If true then pick from a preselected list of galtileids
agn_cache_file: str
sne_cache_file: str
defs_file: str
Returns
-------
updated_catalog:
A new results array with lens systems added.
"""
twinklesDir = getPackageDir('Twinkles')
om10_cat = os.path.join(twinklesDir, 'data', om10_cat)
self.catalog = catsim_cat
# ****** THIS ASSUMES THAT THE ENVIRONMENT VARIABLE OM10_DIR IS SET *******
lensdb = om10.DB(catalog=om10_cat, vb=False)
self.lenscat = lensdb.lenses.copy()
self.density_param = density_param
self.bandpassDict = BandpassDict.loadTotalBandpassesFromFiles(
bandpassNames=['i'])
self.sne_catalog = pd.read_csv(
os.path.join(twinklesDir, 'data', sne_cat))
#self.sne_catalog = self.sne_catalog.iloc[:101] ### Remove this after testing
self.used_systems = []
self.visit_mjd = visit_mjd
self.sn_obj = SNObject(0., 0.)
self.write_dir = specFileMap.subdir_map['(^specFileGLSN)']
self.sed_path = sed_path
self.cached_sprinkling = cached_sprinkling
if self.cached_sprinkling is True:
if ((agn_cache_file is None) | (sne_cache_file is None)):
raise AttributeError(
'Must specify cache files if using cached_sprinkling.')
#agn_cache_file = os.path.join(twinklesDir, 'data', 'test_agn_galtile_cache.csv')
self.agn_cache = pd.read_csv(agn_cache_file)
#sne_cache_file = os.path.join(twinklesDir, 'data', 'test_sne_galtile_cache.csv')
self.sne_cache = pd.read_csv(sne_cache_file)
else:
self.agn_cache = None
self.sne_cache = None
if defs_file is None:
self.defs_file = os.path.join(twinklesDir, 'data',
'catsim_defs.csv')
else:
self.defs_file = defs_file
specFileStart = 'Burst'
for key, val in sorted(iteritems(SpecMap.subdir_map)):
if re.match(key, specFileStart):
galSpecDir = str(val)
self.galDir = str(
getPackageDir('sims_sed_library') + '/' + galSpecDir + '/')
self.imSimBand = Bandpass()
self.imSimBand.imsimBandpass()
#self.LRG_name = 'Burst.25E09.1Z.spec'
#self.LRG = Sed()
#self.LRG.readSED_flambda(str(galDir + self.LRG_name))
#return
#Calculate imsimband magnitudes of source galaxies for matching
agn_fname = str(
getPackageDir('sims_sed_library') + '/agnSED/agn.spec.gz')
src_iband = self.lenscat['MAGI_IN']
src_z = self.lenscat['ZSRC']
self.src_mag_norm = []
for src, s_z in zip(src_iband, src_z):
agn_sed = Sed()
agn_sed.readSED_flambda(agn_fname)
agn_sed.redshiftSED(s_z, dimming=True)
self.src_mag_norm.append(matchBase().calcMagNorm(
[src], agn_sed, self.bandpassDict))
#self.src_mag_norm = matchBase().calcMagNorm(src_iband,
# [agn_sed]*len(src_iband),
#
# self.bandpassDict)
self.defs_dict = {}
with open(self.defs_file, 'r') as f:
for line in f:
line_defs = line.split(',')
if len(line_defs) > 1:
self.defs_dict[line_defs[0]] = line_defs[1].split('\n')[0]
class sprinkler():
def __init__(self,
catsim_cat,
visit_mjd,
specFileMap,
sed_path,
om10_cat='twinkles_lenses_v2.fits',
sne_cat='dc2_sne_cat.csv',
density_param=1.,
cached_sprinkling=False,
agn_cache_file=None,
sne_cache_file=None,
defs_file=None):
"""
Parameters
----------
catsim_cat: catsim catalog
The results array from an instance catalog.
visit_mjd: float
The mjd of the visit
specFileMap:
This will tell the instance catalog where to write the files
om10_cat: optional, defaults to 'twinkles_lenses_v2.fits
fits file with OM10 catalog
sne_cat: optional, defaults to 'dc2_sne_cat.csv'
density_param: `np.float`, optioanl, defaults to 1.0
the fraction of eligible agn objects that become lensed and should
be between 0.0 and 1.0.
cached_sprinkling: boolean
If true then pick from a preselected list of galtileids
agn_cache_file: str
sne_cache_file: str
defs_file: str
Returns
-------
updated_catalog:
A new results array with lens systems added.
"""
twinklesDir = getPackageDir('Twinkles')
om10_cat = os.path.join(twinklesDir, 'data', om10_cat)
self.catalog = catsim_cat
# ****** THIS ASSUMES THAT THE ENVIRONMENT VARIABLE OM10_DIR IS SET *******
lensdb = om10.DB(catalog=om10_cat, vb=False)
self.lenscat = lensdb.lenses.copy()
self.density_param = density_param
self.bandpassDict = BandpassDict.loadTotalBandpassesFromFiles(
bandpassNames=['i'])
self.sne_catalog = pd.read_csv(
os.path.join(twinklesDir, 'data', sne_cat))
#self.sne_catalog = self.sne_catalog.iloc[:101] ### Remove this after testing
self.used_systems = []
self.visit_mjd = visit_mjd
self.sn_obj = SNObject(0., 0.)
self.write_dir = specFileMap.subdir_map['(^specFileGLSN)']
self.sed_path = sed_path
self.cached_sprinkling = cached_sprinkling
if self.cached_sprinkling is True:
if ((agn_cache_file is None) | (sne_cache_file is None)):
raise AttributeError(
'Must specify cache files if using cached_sprinkling.')
#agn_cache_file = os.path.join(twinklesDir, 'data', 'test_agn_galtile_cache.csv')
self.agn_cache = pd.read_csv(agn_cache_file)
#sne_cache_file = os.path.join(twinklesDir, 'data', 'test_sne_galtile_cache.csv')
self.sne_cache = pd.read_csv(sne_cache_file)
else:
self.agn_cache = None
self.sne_cache = None
if defs_file is None:
self.defs_file = os.path.join(twinklesDir, 'data',
'catsim_defs.csv')
else:
self.defs_file = defs_file
specFileStart = 'Burst'
for key, val in sorted(iteritems(SpecMap.subdir_map)):
if re.match(key, specFileStart):
galSpecDir = str(val)
self.galDir = str(
getPackageDir('sims_sed_library') + '/' + galSpecDir + '/')
self.imSimBand = Bandpass()
self.imSimBand.imsimBandpass()
#self.LRG_name = 'Burst.25E09.1Z.spec'
#self.LRG = Sed()
#self.LRG.readSED_flambda(str(galDir + self.LRG_name))
#return
#Calculate imsimband magnitudes of source galaxies for matching
agn_fname = str(
getPackageDir('sims_sed_library') + '/agnSED/agn.spec.gz')
src_iband = self.lenscat['MAGI_IN']
src_z = self.lenscat['ZSRC']
self.src_mag_norm = []
for src, s_z in zip(src_iband, src_z):
agn_sed = Sed()
agn_sed.readSED_flambda(agn_fname)
agn_sed.redshiftSED(s_z, dimming=True)
self.src_mag_norm.append(matchBase().calcMagNorm(
[src], agn_sed, self.bandpassDict))
#self.src_mag_norm = matchBase().calcMagNorm(src_iband,
# [agn_sed]*len(src_iband),
#
# self.bandpassDict)
self.defs_dict = {}
with open(self.defs_file, 'r') as f:
for line in f:
line_defs = line.split(',')
if len(line_defs) > 1:
self.defs_dict[line_defs[0]] = line_defs[1].split('\n')[0]
def sprinkle(self):
# Define a list that we can write out to a text file
lenslines = []
# For each galaxy in the catsim catalog
updated_catalog = self.catalog.copy()
# print("Running sprinkler. Catalog Length: ", len(self.catalog))
for rowNum, row in enumerate(self.catalog):
# if rowNum == 100 or rowNum % 100000==0:
# print("Gone through ", rowNum, " lines of catalog.")
if not np.isnan(row[self.defs_dict['galaxyAgn_magNorm']]):
candidates = self.find_lens_candidates(
row[self.defs_dict['galaxyAgn_redshift']],
row[self.defs_dict['galaxyAgn_magNorm']])
#varString = json.loads(row[self.defs_dict['galaxyAgn_varParamStr']])
# varString[self.defs_dict['pars']]['t0_mjd'] = 59300.0
#row[self.defs_dict['galaxyAgn_varParamStr']] = json.dumps(varString)
np.random.seed(row[self.defs_dict['galtileid']] % (2 ^ 32 - 1))
pick_value = np.random.uniform()
# If there aren't any lensed sources at this redshift from OM10 move on the next object
if (((len(candidates) > 0) and
(pick_value <= self.density_param) and
(self.cached_sprinkling is False)) |
((self.cached_sprinkling is True) and
(row[self.defs_dict['galtileid']]
in self.agn_cache['galtileid'].values))):
# Randomly choose one the lens systems
# (can decide with or without replacement)
# Sort first to make sure the same choice is made every time
if self.cached_sprinkling is True:
twinkles_sys_cache = self.agn_cache.query(
'galtileid == %i' %
row[self.defs_dict['galtileid']]
)['twinkles_system'].values[0]
newlens = self.lenscat[np.where(
self.lenscat['twinklesId'] == twinkles_sys_cache)
[0]][0]
else:
candidates = candidates[np.argsort(
candidates['twinklesId'])]
newlens = np.random.choice(candidates)
# Append the lens galaxy
# For each image, append the lens images
for i in range(newlens['NIMG']):
lensrow = row.copy()
# XIMG and YIMG are in arcseconds
# raPhSim and decPhoSim are in radians
#Shift all parts of the lensed object, not just its agn part
for lensPart in [
'galaxyBulge', 'galaxyDisk', 'galaxyAgn'
]:
lens_ra = lensrow[self.defs_dict[str(lensPart +
'_raJ2000')]]
lens_dec = lensrow[self.defs_dict[str(
lensPart + '_decJ2000')]]
delta_ra = np.radians(
newlens['XIMG'][i] / 3600.0) / np.cos(lens_dec)
delta_dec = np.radians(newlens['YIMG'][i] / 3600.0)
lensrow[self.defs_dict[str(
lensPart + '_raJ2000')]] = lens_ra + delta_ra
lensrow[self.defs_dict[
str(lensPart +
'_decJ2000')]] = lens_dec + delta_dec
mag_adjust = 2.5 * np.log10(np.abs(newlens['MAG'][i]))
lensrow[
self.defs_dict['galaxyAgn_magNorm']] -= mag_adjust
varString = json.loads(
lensrow[self.defs_dict['galaxyAgn_varParamStr']])
varString[self.defs_dict['pars']]['t0Delay'] = newlens[
'DELAY'][i]
varString[self.defs_dict[
'varMethodName']] = 'applyAgnTimeDelay'
lensrow[self.defs_dict[
'galaxyAgn_varParamStr']] = json.dumps(varString)
lensrow[self.defs_dict['galaxyDisk_majorAxis']] = 0.0
lensrow[self.defs_dict['galaxyDisk_minorAxis']] = 0.0
lensrow[
self.defs_dict['galaxyDisk_positionAngle']] = 0.0
lensrow[self.defs_dict['galaxyDisk_internalAv']] = 0.0
lensrow[self.defs_dict[
'galaxyDisk_magNorm']] = 999. #np.nan To be fixed post run1.1
lensrow[
self.defs_dict['galaxyDisk_sedFilename']] = None
lensrow[self.defs_dict['galaxyBulge_majorAxis']] = 0.0
lensrow[self.defs_dict['galaxyBulge_minorAxis']] = 0.0
lensrow[
self.defs_dict['galaxyBulge_positionAngle']] = 0.0
lensrow[self.defs_dict['galaxyBulge_internalAv']] = 0.0
lensrow[self.defs_dict[
'galaxyBulge_magNorm']] = 999. #np.nan To be fixed post run1.1
lensrow[
self.defs_dict['galaxyBulge_sedFilename']] = None
lensrow[self.defs_dict[
'galaxyBulge_redshift']] = newlens['ZSRC']
lensrow[self.defs_dict[
'galaxyDisk_redshift']] = newlens['ZSRC']
lensrow[self.defs_dict[
'galaxyAgn_redshift']] = newlens['ZSRC']
#To get back twinklesID in lens catalog from phosim catalog id number
#just use np.right_shift(phosimID-28, 10). Take the floor of the last
#3 numbers to get twinklesID in the twinkles lens catalog and the remainder is
#the image number minus 1.
lensrow[self.defs_dict['galtileid']] = (
lensrow[self.defs_dict['galtileid']] * 10000 +
newlens['twinklesId'] * 4 + i)
updated_catalog = np.append(updated_catalog, lensrow)
#Now manipulate original entry to be the lens galaxy with desired properties
#Start by deleting Disk and AGN properties
if not np.isnan(row[self.defs_dict['galaxyDisk_magNorm']]):
row[self.defs_dict['galaxyDisk_majorAxis']] = 0.0
row[self.defs_dict['galaxyDisk_minorAxis']] = 0.0
row[self.defs_dict['galaxyDisk_positionAngle']] = 0.0
row[self.defs_dict['galaxyDisk_internalAv']] = 0.0
row[self.defs_dict[
'galaxyDisk_magNorm']] = 999. #np.nan To be fixed post run1.1
row[self.defs_dict['galaxyDisk_sedFilename']] = None
row[self.defs_dict[
'galaxyAgn_magNorm']] = None #np.nan To be fixed post run1.1
row[self.defs_dict[
'galaxyDisk_magNorm']] = 999. # To be fixed in run1.1
row[self.defs_dict['galaxyAgn_sedFilename']] = None
#Now insert desired Bulge properties
row[self.defs_dict['galaxyBulge_sedFilename']] = newlens[
'lens_sed']
row[self.
defs_dict['galaxyBulge_redshift']] = newlens['ZLENS']
row[self.
defs_dict['galaxyDisk_redshift']] = newlens['ZLENS']
row[self.
defs_dict['galaxyAgn_redshift']] = newlens['ZLENS']
row_lens_sed = Sed()
row_lens_sed.readSED_flambda(
str(self.galDir + newlens['lens_sed']))
row_lens_sed.redshiftSED(newlens['ZLENS'], dimming=True)
row[self.defs_dict['galaxyBulge_magNorm']] = matchBase(
).calcMagNorm(
[newlens['APMAG_I']], row_lens_sed,
self.bandpassDict) #Changed from i band to imsimband
row[self.defs_dict[
'galaxyBulge_majorAxis']] = radiansFromArcsec(
newlens['REFF'] / np.sqrt(1 - newlens['ELLIP']))
row[self.defs_dict[
'galaxyBulge_minorAxis']] = radiansFromArcsec(
newlens['REFF'] * np.sqrt(1 - newlens['ELLIP']))
#Convert orientation angle to west of north from east of north by *-1.0 and convert to radians
row[self.defs_dict['galaxyBulge_positionAngle']] = newlens[
'PHIE'] * (-1.0) * np.pi / 180.0
#Replace original entry with new entry
updated_catalog[rowNum] = row
else:
if self.cached_sprinkling is True:
if row[self.defs_dict['galtileid']] in self.sne_cache[
'galtileid'].values:
use_system = self.sne_cache.query(
'galtileid == %i' %
row[self.defs_dict['galtileid']]
)['twinkles_system'].values
use_df = self.sne_catalog.query(
'twinkles_sysno == %i' % use_system)
self.used_systems.append(use_system)
else:
continue
else:
lens_sne_candidates = self.find_sne_lens_candidates(
row[self.defs_dict['galaxyDisk_redshift']])
candidate_sysno = np.unique(
lens_sne_candidates['twinkles_sysno'])
num_candidates = len(candidate_sysno)
if num_candidates == 0:
continue
used_already = np.array([
sys_num in self.used_systems
for sys_num in candidate_sysno
])
unused_sysno = candidate_sysno[~used_already]
if len(unused_sysno) == 0:
continue
np.random.seed(row[self.defs_dict['galtileid']] %
(2 ^ 32 - 1))
use_system = np.random.choice(unused_sysno)
use_df = self.sne_catalog.query('twinkles_sysno == %i' %
use_system)
for i in range(len(use_df)):
lensrow = row.copy()
for lensPart in ['galaxyBulge', 'galaxyDisk', 'galaxyAgn']:
lens_ra = lensrow[self.defs_dict[str(lensPart +
'_raJ2000')]]
lens_dec = lensrow[self.defs_dict[str(lensPart +
'_decJ2000')]]
delta_ra = np.radians(
use_df['x'].iloc[i] / 3600.0) / np.cos(lens_dec)
delta_dec = np.radians(use_df['y'].iloc[i] / 3600.0)
lensrow[self.defs_dict[str(
lensPart + '_raJ2000')]] = lens_ra + delta_ra
lensrow[self.defs_dict[str(
lensPart + '_decJ2000')]] = lens_dec + delta_dec
# varString = json.loads(lensrow[self.defs_dict['galaxyAgn_varParamStr']])
varString = 'None'
lensrow[
self.defs_dict['galaxyAgn_varParamStr']] = varString
lensrow[self.defs_dict['galaxyDisk_majorAxis']] = 0.0
lensrow[self.defs_dict['galaxyDisk_minorAxis']] = 0.0
lensrow[self.defs_dict['galaxyDisk_positionAngle']] = 0.0
lensrow[self.defs_dict['galaxyDisk_internalAv']] = 0.0
lensrow[self.defs_dict[
'galaxyDisk_magNorm']] = 999. #np.nan To be fixed post run1.1
lensrow[self.defs_dict['galaxyDisk_sedFilename']] = None
lensrow[self.defs_dict['galaxyBulge_majorAxis']] = 0.0
lensrow[self.defs_dict['galaxyBulge_minorAxis']] = 0.0
lensrow[self.defs_dict['galaxyBulge_positionAngle']] = 0.0
lensrow[self.defs_dict['galaxyBulge_internalAv']] = 0.0
lensrow[self.defs_dict[
'galaxyBulge_magNorm']] = 999. #np.nan To be fixed post run1.1
lensrow[self.defs_dict['galaxyBulge_sedFilename']] = None
z_s = use_df['zs'].iloc[i]
lensrow[self.defs_dict['galaxyBulge_redshift']] = z_s
lensrow[self.defs_dict['galaxyDisk_redshift']] = z_s
lensrow[self.defs_dict['galaxyAgn_redshift']] = z_s
#To get back twinklesID in lens catalog from phosim catalog id number
#just use np.right_shift(phosimID-28, 10). Take the floor of the last
#3 numbers to get twinklesID in the twinkles lens catalog and the remainder is
#the image number minus 1.
lensrow[self.defs_dict['galtileid']] = (
lensrow[self.defs_dict['galtileid']] * 10000 +
use_system * 4 + i)
add_to_cat, sn_magnorm, sn_fname = self.create_sn_sed(
use_df.iloc[i],
lensrow[self.defs_dict['galaxyAgn_raJ2000']],
lensrow[self.defs_dict['galaxyAgn_decJ2000']],
self.visit_mjd)
lensrow[self.defs_dict['galaxyAgn_sedFilename']] = sn_fname
lensrow[self.defs_dict[
'galaxyAgn_magNorm']] = sn_magnorm #This will need to be adjusted to proper band
mag_adjust = 2.5 * np.log10(np.abs(use_df['mu'].iloc[i]))
lensrow[self.defs_dict['galaxyAgn_magNorm']] -= mag_adjust
if add_to_cat is True:
updated_catalog = np.append(updated_catalog, lensrow)
else:
continue
#Now manipulate original entry to be the lens galaxy with desired properties
#Start by deleting Disk and AGN properties
if not np.isnan(row[self.defs_dict['galaxyDisk_magNorm']]):
row[self.defs_dict['galaxyDisk_majorAxis']] = 0.0
row[self.defs_dict['galaxyDisk_minorAxis']] = 0.0
row[self.defs_dict['galaxyDisk_positionAngle']] = 0.0
row[self.defs_dict['galaxyDisk_internalAv']] = 0.0
row[self.defs_dict[
'galaxyDisk_magNorm']] = 999. #np.nan To be fixed post run1.1
row[self.defs_dict['galaxyDisk_sedFilename']] = None
row[self.defs_dict[
'galaxyAgn_magNorm']] = None #np.nan To be fixed post run1.1
row[self.defs_dict[
'galaxyDisk_magNorm']] = 999. #To be fixed post run1.1
row[self.defs_dict['galaxyAgn_sedFilename']] = None
#Now insert desired Bulge properties
row[self.defs_dict['galaxyBulge_sedFilename']] = use_df[
'lens_sed'].iloc[0]
row[self.
defs_dict['galaxyBulge_redshift']] = use_df['zl'].iloc[0]
row[self.
defs_dict['galaxyDisk_redshift']] = use_df['zl'].iloc[0]
row[self.
defs_dict['galaxyAgn_redshift']] = use_df['zl'].iloc[0]
row[self.defs_dict['galaxyBulge_magNorm']] = use_df[
'bulge_magnorm'].iloc[0]
# row[self.defs_dict['galaxyBulge_magNorm']] = matchBase().calcMagNorm([newlens['APMAG_I']], self.LRG, self.bandpassDict) #Changed from i band to imsimband
row[self.
defs_dict['galaxyBulge_majorAxis']] = radiansFromArcsec(
use_df['r_eff'].iloc[0] /
np.sqrt(1 - use_df['e'].iloc[0]))
row[self.
defs_dict['galaxyBulge_minorAxis']] = radiansFromArcsec(
use_df['r_eff'].iloc[0] *
np.sqrt(1 - use_df['e'].iloc[0]))
#Convert orientation angle to west of north from east of north by *-1.0 and convert to radians
row[self.defs_dict['galaxyBulge_positionAngle']] = use_df[
'theta_e'].iloc[0] * (-1.0) * np.pi / 180.0
#Replace original entry with new entry
updated_catalog[rowNum] = row
return updated_catalog
def find_lens_candidates(self, galz, gal_mag):
# search the OM10 catalog for all sources +- 0.1 dex in redshift
# and within .25 mags of the CATSIM source
w = np.where(
(np.abs(np.log10(self.lenscat['ZSRC']) - np.log10(galz)) <= 0.1)
& (np.abs(self.src_mag_norm - gal_mag) <= .25))[0]
lens_candidates = self.lenscat[w]
return lens_candidates
def find_sne_lens_candidates(self, galz):
w = np.where(
(np.abs(np.log10(self.sne_catalog['zs']) - np.log10(galz)) <= 0.1))
lens_candidates = self.sne_catalog.iloc[w]
return lens_candidates
def create_sn_sed(self, system_df, sn_ra, sn_dec, sed_mjd):
sn_param_dict = copy.deepcopy(self.sn_obj.SNstate)
sn_param_dict['_ra'] = sn_ra
sn_param_dict['_dec'] = sn_dec
sn_param_dict['z'] = system_df['zs']
sn_param_dict['c'] = system_df['c']
sn_param_dict['x0'] = system_df['x0']
sn_param_dict['x1'] = system_df['x1']
sn_param_dict['t0'] = system_df['t_start']
# sn_param_dict['t0'] = 61681.083859 #+1500. ### For testing only
current_sn_obj = self.sn_obj.fromSNState(sn_param_dict)
current_sn_obj.mwEBVfromMaps()
wavelen_max = 1800.
wavelen_min = 30.
wavelen_step = 0.1
sn_sed_obj = current_sn_obj.SNObjectSED(time=sed_mjd,
wavelen=np.arange(
wavelen_min, wavelen_max,
wavelen_step))
flux_500 = sn_sed_obj.flambda[np.where(
sn_sed_obj.wavelen >= 499.99)][0]
if flux_500 > 0.:
add_to_cat = True
sn_magnorm = current_sn_obj.catsimBandMag(self.imSimBand, sed_mjd)
sn_name = 'specFileGLSN_%i_%i_%.4f.txt' % (
system_df['twinkles_sysno'], system_df['imno'], sed_mjd)
sed_filename = '%s/%s' % (self.sed_path, sn_name)
sn_sed_obj.writeSED(sed_filename)
with open(sed_filename,
'rb') as f_in, gzip.open(str(sed_filename + '.gz'),
'wb') as f_out:
shutil.copyfileobj(f_in, f_out)
os.remove(sed_filename)
else:
add_to_cat = False
sn_magnorm = np.nan
sn_name = None
return add_to_cat, sn_magnorm, sn_name
def update_catsim(self):
# Remove the catsim object
# Add lensed images to the catsim given source brightness and magnifications
# Add lens galaxy to catsim
return
def catsim_to_phosim(self):
# Pass this catsim to phosim to make images
return
def main(ramax=58, ramin=56, decmin=-32, decmax=-31, t0=59215, tm=61406):
query = query_tmpl.format(ramin, ramax, decmin, decmax)
sntab = pd.read_sql_query(query, conn)
#sntab.to_csv('./catalogs+tables/sn_cat_rectangle.csv')
#if os.path.isfile('./catalogs+tables/full_t_visits_from_minion.csv'):
# visitab = pd.read_csv('./catalogs+tables/full_t_visits_from_minion.csv')
#else:
res = ObsMetaData.getObservationMetaData(boundLength=2,
boundType='circle',
fieldRA=(ramin - 3, ramax + 3),
fieldDec=(decmin - 3, decmax + 3),
expMJD=(t0, tm))
parsed = [Odict(obsmd.summary['OpsimMetaData']) for obsmd in res]
for obsmd, summ in zip(res, parsed):
ditherRa = np.rad2deg(summ['descDitheredRA'])
ditherDec = np.rad2deg(summ['descDitheredDec'])
ditherRot = np.rad2deg(summ['descDitheredRotTelPos'])
summ['descDitheredRotSkyPos'] = getRotSkyPos(ditherRa, ditherDec,
obsmd, ditherRot)
df = pd.DataFrame(parsed)
df = df[df['filter'].isin(('g', 'r', 'i', 'z'))]
X = df[[
'obsHistID', 'filter', 'FWHMeff', 'descDitheredRA', 'descDitheredDec',
'descDitheredRotTelPos', 'airmass', 'fiveSigmaDepth', 'expMJD',
'descDitheredRotSkyPos', 'fieldRA', 'fieldDec', 'rotSkyPos',
'rotTelPos'
]].copy()
X.descDitheredRA = np.rad2deg(X.descDitheredRA)
X.descDitheredDec = np.rad2deg(X.descDitheredDec)
X.descDitheredRotTelPos = np.rad2deg(X.descDitheredRotTelPos)
#X.descDitheredRotSkyPos = np.rad2deg(X.descDitheredRotSkyPos) already in deg
X.fieldRA = np.rad2deg(X.fieldRA)
X.fieldDec = np.rad2deg(X.fieldDec)
X.rotTelPos = np.rad2deg(X.rotTelPos)
X.rotSkyPos = np.rad2deg(X.rotSkyPos)
X['d1'] = angularSeparation(ramin, decmax, X.descDitheredRA.values,
X.descDitheredDec.values)
X['d2'] = angularSeparation(ramin, decmin, X.descDitheredRA.values,
X.descDitheredDec.values)
X['d3'] = angularSeparation(ramax, decmax, X.descDitheredRA.values,
X.descDitheredDec.values)
X['d4'] = angularSeparation(ramax, decmin, X.descDitheredRA.values,
X.descDitheredDec.values)
visitab = X.query('d1 < 1.75 | d2 < 1.75 | d3 < 1.75 |d4 < 1.75')
del (X)
del (df)
visitab.to_csv('./catalogs+tables/full_t_visits_from_minion.csv')
# setting the observation telescope status
boresight = []
orientation = []
wcs_list = []
for avisit in visitab.itertuples():
bsight = geom.SpherePoint(avisit.descDitheredRA * geom.degrees,
avisit.descDitheredDec * geom.degrees)
orient = (90 - avisit.descDitheredRotSkyPos) * geom.degrees
wcs_list.append([
makeSkyWcs(t,
orient,
flipX=False,
boresight=bsight,
projection='TAN') for t in trans
])
orientation.append(orient)
boresight.append(bsight)
times = visitab['expMJD']
bands = visitab['filter']
depths = visitab['fiveSigmaDepth']
#colnames = ['mjd', 'filter']
data_cols = {'mjd': times, 'filter': bands, 'visitn': visitab['obsHistID']}
n_observ = []
n_trueobserv = []
for asn in sntab.itertuples():
sn_mod = SNObject(ra=asn.snra_in, dec=asn.sndec_in)
sn_mod.set(z=asn.z_in,
t0=asn.t0_in,
x1=asn.x1_in,
c=asn.c_in,
x0=asn.x0_in)
sn_skyp = afwGeom.SpherePoint(asn.snra_in, asn.sndec_in,
afwGeom.degrees)
size = len(times)
sn_flxs = np.zeros(size)
sn_mags = np.zeros(size)
sn_flxe = np.zeros(size)
sn_mage = np.zeros(size)
sn_obsrvd = []
sn_observable = []
ii = 0
for mjd, filt, wcsl, m5 in zip(times, bands, wcs_list, depths):
flux = sn_mod.catsimBandFlux(mjd, LSST_BPass[filt])
mag = sn_mod.catsimBandMag(LSST_BPass[filt], mjd, flux)
flux_er = sn_mod.catsimBandFluxError(mjd, LSST_BPass[filt], m5,
flux)
mag_er = sn_mod.catsimBandMagError(mjd,
LSST_BPass[filt],
m5,
magnitude=mag)
# checking sensors containing this object
contain = [box.contains(afwGeom.Point2I(wcs.skyToPixel(sn_skyp))) \
for box, wcs in zip(boxes, wcsl)]
observed = np.sum(contain) > 0
observable = observed & (flux > 0.0
) #(mag + mag_er < 27.0) & (mag_er < 0.5)
# if observed:
# print('Overlaps ccd', names[np.where(contain)[0][0]])
sn_observable.append(observable)
sn_obsrvd.append(observed)
sn_flxs[ii] = flux # done
sn_mags[ii] = mag
sn_flxe[ii] = flux_er
sn_mage[ii] = mag_er
ii += 1
data_cols[asn.snid_in + '_observable'] = sn_observable
data_cols[asn.snid_in + '_observed'] = sn_obsrvd
data_cols[asn.snid_in + '_flux'] = sn_flxs
data_cols[asn.snid_in + '_fluxErr'] = sn_flxe
data_cols[asn.snid_in + '_mag'] = sn_mags
data_cols[asn.snid_in + '_magErr'] = sn_mage
n_observ.append(np.sum(sn_obsrvd))
n_trueobserv.append(np.sum(sn_observable))
sntab['Nobserv'] = n_observ
sntab['N_trueobserv'] = n_trueobserv
lightcurves = pd.DataFrame(data_cols)
dest_lc = './lightcurves/lightcurves_cat_rect_{}_{}_{}_{}.csv'
lightcurves.to_csv(dest_lc.format(ramax, ramin, decmax, decmin))
dest_snfile = './catalogs+tables/supernovae_cat_rect_{}_{}_{}_{}.csv'
sntab.to_csv(dest_snfile.format(ramax, ramin, decmax, decmin))
print("""Stored the lightcurves in {},
the SN catalog in {}""".format(
dest_lc.format(ramax, ramin, decmax, decmin),
dest_snfile.format(ramax, ramin, decmax, decmin)))
return
class SNObject_tests(unittest.TestCase):
def setUp(self):
"""
Setup tests
SN_blank: A SNObject with no MW extinction
"""
from astropy.config import get_config_dir
mydir = get_config_dir()
print '==============================='
print '==============================='
print (mydir)
print '==============================='
print '==============================='
# A range of wavelengths in Ang
self.wave = np.arange(3000., 12000., 50.)
# Equivalent wavelenths in nm
self.wavenm = self.wave / 10.
# Time to be used as Peak
self.mjdobs = 571190
# Check that we can set up a SED
# with no extinction
self.SN_blank = SNObject()
self.SN_blank.setCoords(ra=30., dec=-60.)
self.SN_blank.set(z=0.96, t0=571181, x1=2.66, c=0.353, x0=1.796e-6)
self.SN_blank.set_MWebv(0.)
self.SN_extincted = SNObject(ra=30., dec=-60.)
self.SN_extincted.set(z=0.96, t0=571181, x1=2.66, c=0.353,
x0=1.796112e-06)
self.SNCosmoModel = self.SN_extincted.equivalentSNCosmoModel()
self.lsstBandPass = BandpassDict.loadTotalBandpassesFromFiles()
self.SNCosmoBP = sncosmo.Bandpass(wave=self.lsstBandPass['r'].wavelen,
trans=self.lsstBandPass['r'].sb,
wave_unit=astropy.units.Unit('nm'),
name='lsst_r')
def tearDown(self):
pass
def test_SNstatenotEmpty(self):
"""
Check that the state of SNObject, stored in self.SNstate has valid
entries for all keys and does not contain keys with None type Values.
"""
myDict = self.SN_extincted.SNstate
for key in myDict.keys():
assert myDict[key] is not None
def test_ComparebandFluxes2photUtils(self):
"""
The SNObject.catsimBandFlux computation uses the sims.photUtils.sed
band flux computation under the hood. This test makes sure that these
definitions are in sync
"""
snobject_r = self.SN_extincted.catsimBandFlux(
bandpassobject=self.lsstBandPass['r'],
time=self.mjdobs)
# `sims.photUtils.Sed`
sed = self.SN_extincted.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandPass['r'])
sedflux = sed.calcFlux(bandpass=self.lsstBandPass['r'])
np.testing.assert_allclose(snobject_r, sedflux / 3631.0)
def test_CompareBandFluxes2SNCosmo(self):
"""
Compare the r band flux at a particular time computed in SNObject and
SNCosmo for MW-extincted SEDs. While the underlying sed is obtained
from SNCosmo the integration with the bandpass is an independent
calculation in SNCosmo and catsim
"""
times = self.mjdobs
catsim_r = self.SN_extincted.catsimBandFlux(
bandpassobject=self.lsstBandPass['r'],
time=times)
sncosmo_r = self.SNCosmoModel.bandflux(band=self.SNCosmoBP,
time=times, zpsys='ab',
zp=0.)
np.testing.assert_allclose(sncosmo_r, catsim_r)
def test_CompareBandMags2SNCosmo(self):
"""
Compare the r band flux at a particular time computed in SNObject and
SNCosmo for MW-extincted SEDs. Should work whenever the flux comparison
above works.
"""
times = self.mjdobs
catsim_r = self.SN_extincted.catsimBandMag(
bandpassobject=self.lsstBandPass['r'],
time=times)
sncosmo_r = self.SNCosmoModel.bandmag(band=self.SNCosmoBP,
time=times, magsys='ab')
np.testing.assert_allclose(sncosmo_r, catsim_r)
def test_CompareExtinctedSED2SNCosmo(self):
"""
Compare the extincted SEDS in SNCosmo and SNObject. Slightly more
non-trivial than comparing unextincted SEDS, as the extinction in
SNObject uses different code from SNCosmo. However, this is still
using the same values of MWEBV, rather than reading it off a map.
"""
SNObjectSED = self.SN_extincted.SNObjectSED(time=self.mjdobs,
wavelen=self.wavenm)
SNCosmoSED = self.SNCosmoModel.flux(time=self.mjdobs, wave=self.wave) \
* 10.
np.testing.assert_allclose(SNObjectSED.flambda, SNCosmoSED,
rtol=1.0e-7)
def test_CompareUnextinctedSED2SNCosmo(self):
"""
Compares the unextincted flux Densities in SNCosmo and SNObject. This
is mereley a sanity check as SNObject uses SNCosmo under the hood.
"""
SNCosmoFluxDensity = self.SN_blank.flux(wave=self.wave,
time=self.mjdobs) * 10.
unextincted_sed = self.SN_blank.SNObjectSED(time=self.mjdobs,
wavelen=self.wavenm)
SNObjectFluxDensity = unextincted_sed.flambda
np.testing.assert_allclose(SNCosmoFluxDensity, SNObjectFluxDensity,
rtol=1.0e-7)
def get_snbrightness(self):
"""
getters for brightness related parameters of sn
"""
if self._sn_object_cache is None or len(
self._sn_object_cache) > 1000000:
self._sn_object_cache = {}
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
ebv = self.column_by_name('EBV')
id_list = self.column_by_name('snid')
bandname = self.obs_metadata.bandpass
if isinstance(bandname, list):
raise ValueError('bandname expected to be string, but is list\n')
bandpass = self.lsstBandpassDict[bandname]
# Initialize return array so that it contains the values you would get
# if you passed through a t0=self.badvalues supernova
vals = np.array([[0.0] * len(t0), [np.inf] * len(t0),
[np.nan] * len(t0), [np.inf] * len(t0),
[0.0] * len(t0)]).transpose()
for i in np.where(
np.logical_and(
np.isfinite(t0),
np.abs(self.mjdobs - t0) < self.maxTimeSNVisible))[0]:
if id_list[i] in self._sn_object_cache:
SNobject = self._sn_object_cache[id_list[i]]
else:
SNobject = SNObject()
SNobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
SNobject.setCoords(ra=raDeg[i], dec=decDeg[i])
SNobject.set_MWebv(ebv[i])
self._sn_object_cache[id_list[i]] = SNobject
if self.mjdobs <= SNobject.maxtime(
) and self.mjdobs >= SNobject.mintime():
# Calculate fluxes
fluxinMaggies = SNobject.catsimBandFlux(
time=self.mjdobs, bandpassobject=bandpass)
mag = SNobject.catsimBandMag(time=self.mjdobs,
fluxinMaggies=fluxinMaggies,
bandpassobject=bandpass)
vals[i, 0] = fluxinMaggies
vals[i, 1] = mag
flux_err = SNobject.catsimBandFluxError(
time=self.mjdobs,
bandpassobject=bandpass,
m5=self.obs_metadata.m5[bandname],
photParams=self.photometricparameters,
fluxinMaggies=fluxinMaggies,
magnitude=mag)
mag_err = SNobject.catsimBandMagError(
time=self.mjdobs,
bandpassobject=bandpass,
m5=self.obs_metadata.m5[bandname],
photParams=self.photometricparameters,
magnitude=mag)
sed = SNobject.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandpassDict,
applyExtinction=True)
adu = sed.calcADU(bandpass,
photParams=self.photometricparameters)
vals[i, 2] = flux_err
vals[i, 3] = mag_err
vals[i, 4] = adu
return (vals[:, 0], vals[:, 1], vals[:, 2], vals[:, 3], vals[:, 4])
def get_snfluxes(self):
c, x1, x0, t0, _z, ra, dec = self.column_by_name('c'),\
self.column_by_name('x1'),\
self.column_by_name('x0'),\
self.column_by_name('t0'),\
self.column_by_name('redshift'),\
self.column_by_name('raJ2000'),\
self.column_by_name('decJ2000')
raDeg = np.degrees(ra)
decDeg = np.degrees(dec)
snobject = SNObject()
# Initialize return array
vals = np.zeros(shape=(self.numobjs, 19))
for i, _ in enumerate(vals):
snobject.set(z=_z[i], c=c[i], x1=x1[i], t0=t0[i], x0=x0[i])
snobject.setCoords(ra=raDeg[i], dec=decDeg[i])
snobject.mwEBVfromMaps()
# Calculate fluxes
vals[i, :6] = snobject.catsimManyBandFluxes(
time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
observedBandPassInd=None)
# Calculate magnitudes
vals[i, 6:12] = snobject.catsimManyBandMags(
time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
observedBandPassInd=None)
vals[i, 12:18] = snobject.catsimManyBandADUs(
time=self.mjdobs,
bandpassDict=self.lsstBandpassDict,
photParams=self.photometricparameters)
vals[i, 18] = snobject.ebvofMW
return (vals[:, 0], vals[:, 1], vals[:, 2], vals[:, 3], vals[:, 4],
vals[:, 5], vals[:, 6], vals[:, 7], vals[:, 8], vals[:, 9],
vals[:, 10], vals[:, 11], vals[:, 12], vals[:, 13],
vals[:, 14], vals[:, 15], vals[:, 16], vals[:, 17], vals[:,
18])
class SNSynthPhotFactory:
"""
Factory class to return the SyntheticPhotometry objects for a SN Ia
as a function of time. This uses the 'salt2-extended' model in
sncosmo as implemented in sims_catUtils.
"""
lsst_bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
def __init__(self, z=0, t0=0, x0=1, x1=0, c=0, snra=0, sndec=0):
"""
Parameters
----------
z: float [0]
Redshift of the SNIa object to pass to sncosmo.
t0: float [0]
Time in mjd of phase=0, corresponding to the B-band
maximum.
x0: float [1]
Normalization factor for the lightcurves.
x1: float [0]
Empirical parameter controlling the stretch in time of the
light curves
c: float [0]
Empirical parameter controlling the colors.
snra: float [0]
RA in degrees of the SNIa.
sndec: float [0]
Dec in degrees of the SNIa.
"""
self.sn_obj = SNObject(snra, sndec)
self.sn_obj.set(z=z,
t0=t0,
x0=x0,
x1=x1,
c=c,
hostebv=0,
hostr_v=3.1,
mwebv=0,
mwr_v=3.1)
self.bp_dict = self.lsst_bp_dict
def set_bp_dict(self, bp_dict):
"""
Set the bandpass dictionary.
Parameters
----------
bp_dict: lsst.sims.photUtils.BandpassDict
Dictionary containing the bandpasses. If None, the standard
LSST total bandpasses will be used.
"""
self.bp_dict = bp_dict
def create(self, mjd):
"""
Return a SyntheticPhotometry object for the specified time in MJD.
Parameters
----------
mjd: float
Observation time in MJD.
Returns
-------
desc.sims_truthcatalog.SyntheticPhotometry
"""
# Create the Sed object. Milky Way extinction will be
# below, so set applyExtinction=False.
sed = self.sn_obj.SNObjectSED(mjd,
bandpass=self.bp_dict,
applyExtinction=False)
# The redshift was applied to the model SED computed by
# sncosmo in the __init__ function, so set redshift=0 here.
synth_phot = SyntheticPhotometry.create_from_sed(sed, redshift=0)
synth_phot.add_MW_dust(*np.degrees(self.sn_obj.skycoord).flatten())
return synth_phot
def __getattr__(self, attr):
# Pass any attribute access requests to the SNObject instance.
return getattr(self.sn_obj, attr)
def validate_sne(cat_dir, obsid, fov_deg=2.1,
scatter_file=None, vanishing_file=None):
"""
Parameters
----------
cat_dir is the parent dir of $obsid
obsid is the obsHistID of the pointing (an int)
fov_deg is the radius of the field of view in degrees
"""
project_dir = os.path.join('/global/projecta/projectdirs',
'lsst/groups/SSim/DC2/cosmoDC2_v1.1.4')
sne_db_name = os.path.join(project_dir, 'sne_cosmoDC2_v1.1.4_MS_DDF.db')
if not os.path.isfile(sne_db_name):
raise RuntimeError("\n%s\nis not a file" % sne_db_name)
instcat_dir = os.path.join(cat_dir, '%.8d' % obsid)
if not os.path.isdir(instcat_dir):
raise RuntimeError("\n%s\nis not a dir" % instcat_dir)
sne_name = os.path.join(instcat_dir, 'sne_cat_%d.txt.gz' % obsid)
if not os.path.isfile(sne_name):
raise RuntimeError("\n%s\nis not a file" % sne_name)
phosim_name = os.path.join(instcat_dir, 'phosim_cat_%d.txt' % obsid)
if not os.path.isfile(phosim_name):
raise RuntimeError("\n%s\nis not a file" % phosim_name)
sed_dir = os.path.join(instcat_dir, "Dynamic")
if not os.path.isdir(sed_dir):
raise RuntimeError("\n%s\nis not a dir" % sed_dir)
opsim_db = os.path.join("/global/projecta/projectdirs",
"lsst/groups/SSim/DC2",
"minion_1016_desc_dithered_v4_sfd.db")
if not os.path.isfile(opsim_db):
raise RuntimeError("\n%s\nis not a file" % opsim_db)
band_from_int = 'ugrizy'
bandpass = None
with open(phosim_name, 'r') as in_file:
for line in in_file:
params = line.strip().split()
if params[0] == 'filter':
bandpass = band_from_int[int(params[1])]
break
if bandpass is None:
raise RuntimeError("Failed to read in bandpass")
bp_dict = photUtils.BandpassDict.loadTotalBandpassesFromFiles()
with sqlite3.connect(opsim_db) as conn:
c = conn.cursor()
r = c.execute("SELECT descDitheredRA, descDitheredDec, expMJD FROM Summary "
"WHERE obsHistID==%d" % obsid).fetchall()
pointing_ra = np.degrees(r[0][0])
pointing_dec = np.degrees(r[0][1])
expmjd = float(r[0][2])
with sqlite3.connect(sne_db_name) as conn:
c = conn.cursor()
query = "SELECT snid_in, snra_in, sndec_in, "
query += "c_in, mB, t0_in, x0_in, x1_in, z_in "
query += "FROM sne_params WHERE ("
where_clause = None
half_space = htm.halfSpaceFromRaDec(pointing_ra, pointing_dec, fov_deg)
bounds = half_space.findAllTrixels(6)
for bound in bounds:
if where_clause is not None:
where_clause += " OR ("
else:
where_clause = "("
if bound[0] == bound[1]:
where_clause += "htmid_level_6==%d" % bound[0]
else:
where_clause += "htmid_level_6>=%d AND htmid_level_6<=%d" % (bound[0],bound[1])
where_clause += ")"
query += where_clause+")"
sn_params = c.execute(query).fetchall()
sn_ra = np.array([sn[1] for sn in sn_params])
sn_dec = np.array([sn[2] for sn in sn_params])
sn_d = angularSeparation(pointing_ra, pointing_dec,
sn_ra, sn_dec)
valid = np.where(sn_d<=fov_deg)
sn_ra_dec = {}
sn_param_dict = {}
for i_sn in valid[0]:
sn = sn_params[i_sn]
sn_param_dict[sn[0]] = sn[3:]
sn_ra_dec[sn[0]] = sn[1:3]
sne_in_instcat = set()
d_mag_max = -1.0
with gzip.open(sne_name, 'rb') as sne_cat_file:
for sne_line in sne_cat_file:
instcat_params = sne_line.strip().split(b' ')
sne_id = instcat_params[1].decode('utf-8')
if sne_id not in sn_param_dict:
try:
sne_id_int = int(sne_id)
assert sne_id_int<1.5e10
except (ValueError, AssertionError):
raise RuntimeError("\n%s\nnot in SNe db" % sne_id)
sne_in_instcat.add(sne_id)
control_params = sn_param_dict[sne_id]
sed_name = os.path.join(instcat_dir, instcat_params[5].decode('utf-8'))
if not os.path.isfile(sed_name):
raise RuntimeError("\n%s\nis not a file" % sed_name)
sed = photUtils.Sed()
sed.readSED_flambda(sed_name, cache_sed=False)
fnorm = photUtils.getImsimFluxNorm(sed, float(instcat_params[4]))
sed.multiplyFluxNorm(fnorm)
sed.redshiftSED(float(instcat_params[6]), dimming=True)
a_x, b_x = sed.setupCCM_ab()
A_v = float(instcat_params[15])
R_v = float(instcat_params[16])
EBV = A_v/R_v
sed.addDust(a_x, b_x, A_v=A_v, R_v=R_v)
sn_object = SNObject()
sn_object.set_MWebv(EBV)
sn_object.set(c=control_params[0], x1=control_params[4],
x0=control_params[3], t0=control_params[2],
z=control_params[5])
sn_mag = sn_object.catsimBandMag(bp_dict[bandpass], expmjd)
instcat_flux = sed.calcFlux(bp_dict[bandpass])
instcat_mag = sed.magFromFlux(instcat_flux)
d_mag = (sn_mag-instcat_mag)
if not np.isfinite(d_mag):
if np.isfinite(sn_mag) or np.isfinite(instcat_mag):
msg = '%s\ngave magnitudes %e %e (diff %e)' % (sne_id,
sn_mag,
instcat_mag,
d_mag)
print(msg)
if scatter_file is not None:
scatter_file.write("%e %e %e\n" % (sn_mag, instcat_mag, d_mag))
d_mag = np.abs(d_mag)
if d_mag>d_mag_max:
d_mag_max = d_mag
#print('dmag %e -- %e (%e)' %
# (d_mag, instcat_mag,
# control_params[5]-float(instcat_params[6])))
msg = '\n%s\n' % sne_name
ct_missing = 0
for sn_id in sn_param_dict:
if sn_id in sne_in_instcat:
continue
control_params = sn_param_dict[sn_id]
sn_object = SNObject()
sn_object.set_MWebv(0.0)
cc = control_params[0]
x1 = control_params[4]
x0 = control_params[3]
t0 = control_params[2]
zz = control_params[5]
sn_object.set(c=cc, x1=x1, x0=x0, t0=t0, z=zz)
sn_mag = sn_object.catsimBandMag(bp_dict[bandpass], expmjd)
if vanishing_file is not None and np.isfinite(sn_mag):
vanishing_file.write('%d %s %s %e ' % (obsid, bandpass, sn_id, sn_mag))
vanishing_file.write('%e %e %e %.4f %e %.4f %e\n' %
(cc,x0,x1,t0,zz,expmjd,expmjd-t0))
class SNObject_tests(unittest.TestCase):
@classmethod
def tearDownClass(cls):
sims_clean_up()
def setUp(self):
"""
Setup tests
SN_blank: A SNObject with no MW extinction
"""
mydir = get_config_dir()
print('===============================')
print('===============================')
print (mydir)
print('===============================')
print('===============================')
# A range of wavelengths in Ang
self.wave = np.arange(3000., 12000., 50.)
# Equivalent wavelenths in nm
self.wavenm = self.wave / 10.
# Time to be used as Peak
self.mjdobs = 571190
# Check that we can set up a SED
# with no extinction
self.SN_blank = SNObject()
self.SN_blank.setCoords(ra=30., dec=-60.)
self.SN_blank.set(z=0.96, t0=571181, x1=2.66, c=0.353, x0=1.796e-6)
self.SN_blank.set_MWebv(0.)
self.SN_extincted = SNObject(ra=30., dec=-60.)
self.SN_extincted.set(z=0.96, t0=571181, x1=2.66, c=0.353,
x0=1.796112e-06)
self.SNCosmoModel = self.SN_extincted.equivalentSNCosmoModel()
self.rectify_photParams = PhotometricParameters()
self.lsstBandPass = BandpassDict.loadTotalBandpassesFromFiles()
self.SNCosmoBP = sncosmo.Bandpass(wave=self.lsstBandPass['r'].wavelen,
trans=self.lsstBandPass['r'].sb,
wave_unit=astropy.units.Unit('nm'),
name='lsst_r')
def tearDown(self):
del self.SNCosmoBP
del self.SN_blank
del self.SN_extincted
def test_SNstatenotEmpty(self):
"""
Check that the state of SNObject, stored in self.SNstate has valid
entries for all keys and does not contain keys with None type Values.
"""
myDict = self.SN_extincted.SNstate
for key in myDict:
assert myDict[key] is not None
def test_attributeDefaults(self):
"""
Check the defaults and the setter properties for rectifySED and
modelOutSideRange
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
self.assertEqual(snobj.rectifySED, True)
self.assertEqual(snobj.modelOutSideTemporalRange, 'zero')
snobj.rectifySED = False
self.assertFalse(snobj.rectifySED, False)
self.assertEqual(snobj.modelOutSideTemporalRange, 'zero')
def test_raisingerror_forunimplementedmodelOutSideRange(self):
"""
check that correct error is raised if the user tries to assign an
un-implemented model value to
`sims.catUtils.supernovae.SNObject.modelOutSideTemporalRange`
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
assert snobj.modelOutSideTemporalRange == 'zero'
with self.assertRaises(ValueError) as context:
snobj.modelOutSideTemporalRange = 'False'
self.assertEqual('Model not implemented, defaulting to zero method\n',
context.exception.args[0])
def test_rectifiedSED(self):
"""
Check for an extreme case that the SN seds are being rectified. This is
done by setting up an extreme case where there will be negative seds, and
checking that this is indeed the case, and checking that they are not
negative if rectified.
"""
snobj = SNObject(ra=30., dec=-60., source='salt2')
snobj.set(z=0.96, t0=self.mjdobs, x1=-3., x0=1.8e-6)
snobj.rectifySED = False
times = np.arange(self.mjdobs - 50., self.mjdobs + 150., 1.)
badTimes = []
for time in times:
sed = snobj.SNObjectSED(time=time,
bandpass=self.lsstBandPass['r'])
if any(sed.flambda < 0.):
badTimes.append(time)
# Check that there are negative SEDs
assert(len(badTimes) > 0)
snobj.rectifySED = True
for time in badTimes:
sed = snobj.SNObjectSED(time=time,
bandpass=self.lsstBandPass['r'])
self.assertGreaterEqual(sed.calcADU(bandpass=self.lsstBandPass['r'],
photParams=self.rectify_photParams), 0.)
self.assertFalse(any(sed.flambda < 0.))
def test_ComparebandFluxes2photUtils(self):
"""
The SNObject.catsimBandFlux computation uses the sims.photUtils.sed
band flux computation under the hood. This test makes sure that these
definitions are in sync
"""
snobject_r = self.SN_extincted.catsimBandFlux(
bandpassobject=self.lsstBandPass['r'],
time=self.mjdobs)
# `sims.photUtils.Sed`
sed = self.SN_extincted.SNObjectSED(time=self.mjdobs,
bandpass=self.lsstBandPass['r'])
sedflux = sed.calcFlux(bandpass=self.lsstBandPass['r'])
np.testing.assert_allclose(snobject_r, sedflux / 3631.0)
def test_CompareBandFluxes2SNCosmo(self):
"""
Compare the r band flux at a particular time computed in SNObject and
SNCosmo for MW-extincted SEDs. While the underlying sed is obtained
from SNCosmo the integration with the bandpass is an independent
calculation in SNCosmo and catsim
"""
times = self.mjdobs
catsim_r = self.SN_extincted.catsimBandFlux(
bandpassobject=self.lsstBandPass['r'],
time=times)
sncosmo_r = self.SNCosmoModel.bandflux(band=self.SNCosmoBP,
time=times, zpsys='ab',
zp=0.)
np.testing.assert_allclose(sncosmo_r, catsim_r)
def test_CompareBandMags2SNCosmo(self):
"""
Compare the r band flux at a particular time computed in SNObject and
SNCosmo for MW-extincted SEDs. Should work whenever the flux comparison
above works.
"""
times = self.mjdobs
catsim_r = self.SN_extincted.catsimBandMag(
bandpassobject=self.lsstBandPass['r'],
time=times)
sncosmo_r = self.SNCosmoModel.bandmag(band=self.SNCosmoBP,
time=times, magsys='ab')
np.testing.assert_allclose(sncosmo_r, catsim_r)
def test_CompareExtinctedSED2SNCosmo(self):
"""
Compare the extincted SEDS in SNCosmo and SNObject. Slightly more
non-trivial than comparing unextincted SEDS, as the extinction in
SNObject uses different code from SNCosmo. However, this is still
using the same values of MWEBV, rather than reading it off a map.
"""
SNObjectSED = self.SN_extincted.SNObjectSED(time=self.mjdobs,
wavelen=self.wavenm)
SNCosmoSED = self.SNCosmoModel.flux(time=self.mjdobs, wave=self.wave) \
* 10.
np.testing.assert_allclose(SNObjectSED.flambda, SNCosmoSED,
rtol=1.0e-7)
def test_CompareUnextinctedSED2SNCosmo(self):
"""
Compares the unextincted flux Densities in SNCosmo and SNObject. This
is mereley a sanity check as SNObject uses SNCosmo under the hood.
"""
SNCosmoFluxDensity = self.SN_blank.flux(wave=self.wave,
time=self.mjdobs) * 10.
unextincted_sed = self.SN_blank.SNObjectSED(time=self.mjdobs,
wavelen=self.wavenm)
SNObjectFluxDensity = unextincted_sed.flambda
np.testing.assert_allclose(SNCosmoFluxDensity, SNObjectFluxDensity,
rtol=1.0e-7)
def test_redshift(self):
"""
test that the redshift method works as expected by checking that
if we redshift a SN from its original redshift orig_z to new_z where
new_z is smaller (larger) than orig_z:
- 1. x0 increases (decreases)
- 2. source peak absolute magnitude in BesselB band stays the same
"""
from astropy.cosmology import FlatLambdaCDM
cosmo = FlatLambdaCDM(H0=70., Om0=0.3)
orig_z = self.SN_extincted.get('z')
orig_x0 = self.SN_extincted.get('x0')
peakabsMag = self.SN_extincted.source_peakabsmag('BessellB', 'AB', cosmo=cosmo)
lowz = orig_z * 0.5
highz = orig_z * 2.0
# Test Case for lower redshift
self.SN_extincted.redshift(z=lowz, cosmo=cosmo)
low_x0 = self.SN_extincted.get('x0')
lowPeakAbsMag = self.SN_extincted.source_peakabsmag('BessellB', 'AB', cosmo=cosmo)
# Test 1.
self.assertGreater(low_x0, orig_x0)
# Test 2.
self.assertAlmostEqual(peakabsMag, lowPeakAbsMag, places=14)
# Test Case for higher redshift
self.SN_extincted.redshift(z=highz, cosmo=cosmo)
high_x0 = self.SN_extincted.get('x0')
HiPeakAbsMag = self.SN_extincted.source_peakabsmag('BessellB', 'AB', cosmo=cosmo)
# Test 1.
self.assertLess(high_x0, orig_x0)
# Test 2.
self.assertAlmostEqual(peakabsMag, HiPeakAbsMag, places=14)
def test_bandFluxErrorWorks(self):
"""
test that bandflux errors work even if the flux is negative
"""
times = self.mjdobs
e = self.SN_extincted.catsimBandFluxError(times,
self.lsstBandPass['r'],
m5=24.5, fluxinMaggies=-1.0)
assert isinstance(e, np.float)
print(e)
assert not(np.isinf(e) or np.isnan(e))
def _light_curves_from_query(self, cat_dict, query_result, grp, lc_per_field=None):
t_dict = {}
gamma_dict = {}
m5_dict = {}
t_min = None
t_max = None
for bp_name in cat_dict:
self.lsstBandpassDict[bp_name].sbTophi()
# generate a 2-D numpy array containing MJDs, m5, and photometric gamma values
# for each observation in the given bandpass
raw_array = np.array([[obs.mjd.TAI, obs.m5[bp_name],
calcGamma(self.lsstBandpassDict[bp_name],
obs.m5[obs.bandpass],
self.phot_params)]
for obs in grp if obs.bandpass == bp_name]).transpose()
if len(raw_array) > 0:
t_dict[bp_name] = raw_array[0]
m5_dict[bp_name] = raw_array[1]
gamma_dict[bp_name] = raw_array[2]
local_t_min = t_dict[bp_name].min()
local_t_max = t_dict[bp_name].max()
if t_min is None or local_t_min < t_min:
t_min = local_t_min
if t_max is None or local_t_max > t_max:
t_max = local_t_max
snobj = SNObject()
cat = cat_dict[list(cat_dict.keys())[0]] # does not need to be associated with a bandpass
dummy_sed = Sed()
n_actual_sn = 0 # how many SN have we actually delivered?
for chunk in query_result:
if lc_per_field is not None and n_actual_sn >= lc_per_field:
break
t_start_chunk = time.time()
for sn in cat.iter_catalog(query_cache=[chunk]):
sn_rng = self.sn_universe.getSN_rng(sn[1])
sn_t0 = self.sn_universe.drawFromT0Dist(sn_rng)
if sn[5] <= self.z_cutoff and np.isfinite(sn_t0) and \
sn_t0 < t_max + cat.maxTimeSNVisible and \
sn_t0 > t_min - cat.maxTimeSNVisible:
sn_c = self.sn_universe.drawFromcDist(sn_rng)
sn_x1 = self.sn_universe.drawFromx1Dist(sn_rng)
sn_x0 = self.sn_universe.drawFromX0Dist(sn_rng, sn_x1, sn_c, sn[4])
snobj.set(t0=sn_t0, c=sn_c, x1=sn_x1, x0=sn_x0, z=sn[5])
for bp_name in t_dict:
t_list = t_dict[bp_name]
m5_list = m5_dict[bp_name]
gamma_list = gamma_dict[bp_name]
bandpass = self.lsstBandpassDict[bp_name]
if len(t_list) == 0:
continue
if snobj.maxtime() >= t_list[0] and snobj.mintime() <= t_list[-1]:
active_dexes = np.where(np.logical_and(t_list >= snobj.mintime(),
t_list <= snobj.maxtime()))
t_active = t_list[active_dexes]
m5_active = m5_list[active_dexes]
gamma_active = gamma_list[active_dexes]
if len(t_active) > 0:
wave_ang = bandpass.wavelen*10.0
mask = np.logical_and(wave_ang > snobj.minwave(),
wave_ang < snobj.maxwave())
wave_ang = wave_ang[mask]
snobj.set(mwebv=sn[6])
sn_ff_buffer = snobj.flux(time=t_active, wave=wave_ang)*10.0
flambda_grid = np.zeros((len(t_active), len(bandpass.wavelen)))
for ff, ff_sn in zip(flambda_grid, sn_ff_buffer):
ff[mask] = np.where(ff_sn > 0.0, ff_sn, 0.0)
fnu_grid = flambda_grid*bandpass.wavelen* \
bandpass.wavelen*dummy_sed._physParams.nm2m* \
dummy_sed._physParams.ergsetc2jansky/dummy_sed._physParams.lightspeed
flux_list = \
(fnu_grid*bandpass.phi).sum(axis=1)*(bandpass.wavelen[1]-bandpass.wavelen[0])
acceptable = np.where(flux_list>0.0)
flux_error_list = flux_list[acceptable]/ \
calcSNR_m5(dummy_sed.magFromFlux(flux_list[acceptable]),
bandpass,
m5_active[acceptable], self.phot_params,
gamma=gamma_active[acceptable])
if len(acceptable) > 0:
n_actual_sn += 1
if lc_per_field is not None and n_actual_sn > lc_per_field:
break
if sn[0] not in self.truth_dict:
self.truth_dict[sn[0]] = {}
self.truth_dict[sn[0]]['t0'] = sn_t0
self.truth_dict[sn[0]]['x1'] = sn_x1
self.truth_dict[sn[0]]['x0'] = sn_x0
self.truth_dict[sn[0]]['c'] = sn_c
self.truth_dict[sn[0]]['z'] = sn[5]
self.truth_dict[sn[0]]['E(B-V)'] = sn[6]
if sn[0] not in self.mjd_dict:
self.mjd_dict[sn[0]] = {}
self.bright_dict[sn[0]] = {}
self.sig_dict[sn[0]] = {}
if bp_name not in self.mjd_dict[sn[0]]:
self.mjd_dict[sn[0]][bp_name] = []
self.bright_dict[sn[0]][bp_name] = []
self.sig_dict[sn[0]][bp_name] = []
for tt, ff, ee in zip(t_active[acceptable], flux_list[acceptable],
flux_error_list[0]):
self.mjd_dict[sn[0]][bp_name].append(tt)
self.bright_dict[sn[0]][bp_name].append(ff/3631.0)
self.sig_dict[sn[0]][bp_name].append(ee/3631.0)
print("chunk of ", len(chunk), " took ", time.time()-t_start_chunk)
reschar = ResChar.fromSNCosmoRes(resfit)
print('fit passed')
except:
reschar = 'failure'
print('failed for SNID {0} with {1} points'.format(
snid, len(lcinstance.snCosmoLC())))
#if reschar != 'failure':
# pass
# fig = None#sncosmo.plot_lc(lcinstance.snCosmoLC(), model=(truth, reschar.sncosmoModel))
return snid, lcinstance, reschar, truth, fig
snidvals = minion_params.index.values
print('The list of SN has {} SN'.format(len(snidvals)))
snmodel = SNObject(ra=30., dec=-30.)
def writevals(snid, fh):
x = inferParams(snid,
snmodel,
paramsDF=minion_params,
lcsDF=minion,
infer_method=sncosmo.fit_lc,
minsnr=0.)
if x[2] != 'failure':
covs = map(str, x[2].covariance.values[np.triu_indices(4)])
params = map(str, x[2].parameters.values)
std = str(x[2].mu_variance_linear()**0.5)
ss = ','.join(params + covs + [std])
# print('cov = ' + ' '.join(covs))