def read_curves_kurtenkov(path=sn_path):
jd = 2457000
lc_data = np.loadtxt(os.path.join(path, 'lrn_aa26564-15_p5.csv'), skiprows=2, usecols=(0, 1, 2, 3),
dtype=[('JD', '<f4'), ('b', '|S1'), ('mag', '<f4'), ('err', '<f4')])
# mshift = 24.43 # Distance Module to M31
curves = SetLightCurve('Red Nova')
bnames = np.unique(lc_data['b'])
for i, n in enumerate(bnames):
b = band.band_by_name(n.decode("utf-8"))
d = lc_data[lc_data['b'] == n, ]
time = d['JD'] + jd
mags = d['mag']
errs = d['err']
# filter bad values
# is_good = mags < 30.
# t = time[is_good]
# mags = mags[is_good]
# errs = errs[is_good]
# add
lc = LightCurve(b, time, mags, errs=errs)
# lc.tshift = -tshift
# lc.mshift = -mshift
curves.add(lc)
return curves
def fit_lc(lc, times=None, Ntime=None, is_RBF=False):
"""
Compute gaussian process for the light curve and return new LC with approximated magnitudes
:param lc: Initial light curve
:param times: new time points [optional, None]
:param Ntime: number point for linspace(min(t), max(t), Ntime) [optional, None]
:param is_RBF: use RationalQuadratic in the kernel
:return:
"""
if is_RBF:
gp = FitGP.lc2gpRBF(lc)
else:
gp = FitGP.lc2gp(lc)
if times is None: # new time points
times = lc.Time
if Ntime is not None:
times = np.linspace(min(times), max(times), Ntime)
if type(times) is not np.ndarray:
times = np.array(times)
if times.ndim == 2:
X_samples = times
else:
X_samples = times.reshape(-1, 1) # 2D array
# Make the prediction on the meshed x-axis (ask for MSE as well)
y_pred, sigma = gp.predict(X_samples, return_std=True)
return LightCurve(lc.Band, times, y_pred, sigma), gp
def load(dic=None):
"""
Load points from dat-files.
:return SetLightCurves:
"""
from pystella.util.math import is_number
fname = None
tshift = 0.
mshift = 0.
mag_lim = 99.
arg = []
is_debug = False
comments = '#'
if dic is not None:
is_debug = dic.get('is_debug', False)
mag_lim = dic.get('mag_lim', mag_lim)
if 'args' in dic:
arg = dic['args']
if len(arg) > 0:
fname = arg.pop(0)
fname = os.path.expanduser(fname)
if len(arg) > 0:
s = arg.pop(0)
if is_number(s):
tshift = float(s)
elif len(arg) > 0:
tshift = float(arg.pop(0))
if len(arg) > 0:
mshift = float(arg.pop(0))
print("Load {0} tshift={1} mshift={2}".format(fname, tshift, mshift))
# read data
# tbl = read_table_header_float(fname)
tbl, cols_data = read_obs_table_header(
fname,
include_names=band.band_get_names_alias(),
is_out=is_debug,
comments=comments)
curves = table2curves(os.path.basename(fname), tbl)
# remove bad data
res_curves = SetLightCurve(curves.Name)
for lc_orig in curves:
is_good = lc_orig.Mag < mag_lim
t = lc_orig.Time[is_good]
m = lc_orig.Mag[is_good]
e = None
if lc_orig.IsErr:
e = lc_orig.Err[is_good]
lc = LightCurve(lc_orig.Band, t, m, e)
res_curves.add(lc)
res_curves.set_tshift(tshift)
res_curves.set_mshift(mshift)
return res_curves
def LCBol(self, time): # todo check this code
from pystella.rf import band
from pystella.rf.lc import LightCurve
b = band.BandUni()
mags = self.MagBol(time)
lc = LightCurve(b, time, mags)
return lc
def table2curves(name,
tbl,
bands=None,
colt=('time', 'JD', 'MJD'),
is_filter_zero=True):
# time = None
for nm in colt:
if nm in tbl.dtype.names:
time = tbl[nm]
break
else:
raise ValueError(
"THe table should contain a column with name in [{0}]".format(
', '.join(colt)))
curves = SetLightCurve(name)
if bands is None:
bands = [n for n in tbl.dtype.names if band.is_exist(n)]
for bname in bands:
b = band.band_by_name(bname)
mag = tbl[bname]
mask = ~np.isnan(mag)
# filter
if is_filter_zero:
mask = np.logical_and(mask,
mag != 0) # filter out values not equal 0
mask = np.logical_and(mask, mag < 99)
t = time[mask]
m = mag[mask]
for err_name in (prefix + bname for prefix in err_prefix):
if err_name in tbl.dtype.names:
err = tbl[err_name]
e = err[mask]
lc = LightCurve(b, t, m, e)
break
else:
lc = LightCurve(b, t, m)
curves.add(lc)
return curves
def read_curves(self):
block = self.load()
header = 'Mbol MU MB MV MI MR'.split()
curves = SetLightCurve(self.name)
time = block['time']
for col in header:
b = band.band_by_name(col.replace('M', ''))
mag = block[col]
lc = LightCurve(b, time, mag)
curves.add(lc)
return curves
def to_curves(self):
ph = pandas.DataFrame.from_dict(self.photometry)
def add(d, k, v):
if k in d:
d[k].append(v)
else:
d[k] = [v]
times = {}
mags = {}
err = {}
# {'magnitude': '6.36', 'u_time': 'MJD', 'time': '46849.44', 'band': 'V', 'source': '44,62'}
if 'e_magnitude' in ph.keys():
for b, t, m, e in zip(ph.band, ph.time, ph.magnitude,
ph.e_magnitude):
add(times, b, t)
add(mags, b, m)
add(err, b, e)
else:
for b, t, m in zip(ph.band, ph.time, ph.magnitude):
add(times, b, t)
add(mags, b, m)
bands = list(times.keys())
band.Band.load_settings()
curves = SetLightCurve(self.Name)
for bname in bands:
if band.is_exist(bname):
tt = list(map(float, times[bname]))
mm = list(map(float, mags[bname]))
if len(err) > 0:
ee = list(map(float, err[bname]))
lc = LightCurve(bname, tt, mm, ee)
else:
lc = LightCurve(bname, tt, mm)
curves.add(lc)
return curves
def read_curves_master(path=sn_path):
header = 'V I R'
bnames = map(str.strip, header.split())
curves = SetLightCurve('Red Nova')
for i, n in enumerate(bnames):
b = band.band_by_name(n)
d = np.loadtxt(os.path.join(path, n + '.txt'),
dtype=[('JD', '<f4'), ('mag', '<f4'), ('err', '<f4')])
time = d['JD']
mags = d['mag']
errs = d['err']
lc = LightCurve(b, time, mags, errs=errs)
curves.add(lc)
return curves
def read_curves_gri(self):
block = self.load(ext='gri', line_header=1)
# header = 'L_bol Mu MB Mg Mr Mi'.split()
# header = 'MB MV'.split()
header = 'L_bol Mu MB MV Mg Mr Mi J H K '.split()
# header = 'MB MV '.split()
# header = 'L_bol L_ubvgri Mu MB MV Mg Mr Mi'.split()
curves = SetLightCurve(self.name)
time = block['time']
for col in header:
b = band.band_by_name(col.replace('M', '').replace('L_', ''))
mag = block[col]
lc = LightCurve(b, time, mag)
curves.add(lc)
return curves
def read_curves(path=sn_path):
header = 'U B V R I'
cols = map(str.strip, header.split())
lc_data = np.loadtxt(os.path.join(path, '1999emubvir.dat'), skiprows=1, usecols=range(1, 12))
time = lc_data[:, 0]
curves = SetLightCurve('Sn99em')
for i, n in enumerate(cols):
b = band.band_by_name(n)
mags = lc_data[:, 2*i+1]
errs = lc_data[:, 2*i+2]
# filter bad values
is_good = mags < 30.
t = time[is_good]
mags = mags[is_good]
errs = errs[is_good]
# add
lc = LightCurve(b, t, mags, errs=errs)
curves.add(lc)
return curves
def flux_to_curve(self, b, z=0., d=0., magnification=1.):
from pystella.rf.lc import LightCurve
if b is None:
raise ValueError("Band must be defined.")
if not self.is_time:
return ValueError("No spectral time points.")
times, mags = self.to_mags(b, z, d, magnification)
times = (1. + z) * np.array(times)
lc = LightCurve(b, times, mags)
lc.attrs('d', d)
lc.attrs('z', z)
lc.attrs('magnification', magnification)
return lc
def read_curves_master_abs_mag(path=sn_path):
jd = 2457036
header = 'V I R'
bnames = map(str.strip, header.split())
curves = SetLightCurve('Red Nova')
for i, n in enumerate(bnames):
b = band.band_by_name(n)
time = np.loadtxt(os.path.join(path, n + '_jd.txt')) + jd
mags = np.loadtxt(os.path.join(path, n + '_mag.txt'))
errs = np.loadtxt(os.path.join(path, n + '_err.txt'))
# filter bad values
# is_good = mags < 30.
# t = time[is_good]
# mags = mags[is_good]
# errs = errs[is_good]
# add
lc = LightCurve(b, time, mags, errs=errs)
curves.add(lc)
return curves
def load(dic=None):
"""
Load points from dat-files.
Reader data-file with mix bname data, like:
>>% head photometry.txt
jd filter mag mage
2457059.6228778586 V 17.493766309999998 0.0592200135089
2457059.6244578934 V 17.539956019999998
0.0542402986717 2457059.6261980557 g 17.782871193345898
0.0454000142503 2457059.6287036575 g 17.7782469177482 0.0395424488201
:return SetLightCurves:
"""
fname = None
tshift = 0.
mshift = 0.
mag_lim = 30.
skiprows = 1.
arg = []
if dic is not None:
mag_lim = dic.get('mag_lim', 30.)
skiprows = dic.get('skiprows', 1)
if 'args' in dic:
arg = dic['args']
if len(arg) > 0:
fname = arg.pop(0)
fname = os.path.expanduser(fname)
if len(arg) > 0:
s = arg.pop(0)
if s.isnumeric():
tshift = float(s)
elif len(arg) > 0:
tshift = float(arg.pop(0))
if len(arg) > 0:
mshift = float(arg.pop(0))
print("Load {0} tshift={1} mshift={2}".format(fname, tshift, mshift))
# read data
dtype = [('time', '<f4'), ('b', 'str'), ('mag', '<f4'), ('err', '<f4')]
# lc_data = np.loadtxt(fname, skiprows=skiprows, dtype=dtype, comments='#') # jd filter mag mage
# lc_data = np.genfromtxt(fname, skip_header=skiprows, dtype=dtype, comments='#') # jd filter mag mage
lc_data = np.genfromtxt(fname,
skip_header=skiprows,
dtype=None,
names=[v[0] for v in dtype],
comments='#')
b_tot = lc_data['b']
bnames = np.unique(b_tot)
curves = SetLightCurve()
for bname in bnames:
if band.is_exist(bname.decode()):
# filter of the current band
d = lc_data[np.where(lc_data['b'] == bname)]
# is_good = list(map(lambda x: x == bname, b_tot))
# t = (lc_data['time'])[is_good]
# m = lc_data['mag'][is_good]
# e = lc_data['err'][is_good]
# add light curve
b = band.band_by_name(bname.decode())
lc = LightCurve(b, d['time'], d['mag'], d['err'])
# lc = LightCurve(b, t, m, e)
curves.add(lc)
else:
print('Could read the light curve. There is no band: {}. '
'You may try to add it to dir data/bands'.format(bname))
# remove bad data
res_curves = SetLightCurve(curves.Name)
for lc_orig in curves:
is_good = lc_orig.Mag < mag_lim
t = lc_orig.Time[is_good]
m = lc_orig.Mag[is_good]
e = None
if lc_orig.IsErr:
e = lc_orig.Err[is_good]
lc = LightCurve(lc_orig.Band, t, m, e)
res_curves.add(lc)
res_curves.set_tshift(tshift)
res_curves.set_mshift(mshift)
return res_curves
def lc_create(bname, m=-19, dt=0.):
n = 10
time = np.linspace(0.+dt, 200.+dt, n)
mags = m * np.ones(n)
return LightCurve(bname, time, mags)
