def __init__(self, b, time, mags, errs=None, tshift=0., mshift=0.):
"""Creates a Light Curve instance. Required parameters: b (band), time, mags."""
if isinstance(b, str): # convert band-name to band instance
if band.is_exist(b):
self._b = band.band_by_name(b)
else:
raise ValueError("No such band: {}".format(b))
else:
self._b = b
super().__init__(self._b.Name, time, mags, errs, tshift=tshift)
self._mshift = mshift
self._attrs = {}
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 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 main():
path = '/home/bakl/Sn/Release/seb_git/res/tt/tanaka'
mname = 'cat_R500_M15_Ni008_E40'
try:
opts, args = getopt.getopt(sys.argv[1:], "hp:i:b:")
except getopt.GetoptError as err:
print(str(err)) # will print something like "option -a not recognized"
usage()
sys.exit(2)
for opt, arg in opts:
if opt == '-i':
mname = str(arg)
break
if opt == '-b':
bands = str(arg).split('-')
for b in bands:
if not band.is_exist(b):
print('No such band: ' + b)
sys.exit(2)
continue
if opt == '-p':
path = str(arg)
if not (os.path.isdir(path) and os.path.exists(path)):
print("No such directory: " + path)
sys.exit(2)
continue
elif opt == '-h':
usage()
sys.exit(2)
compare_ABzVSugri(mname, path)
path = '/home/bakl/Sn/Release/seb_git/res/tt'
compare_ttVSubv(mname, path)
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 curves_read_mix(fname,
dtype=None,
skiprows=1,
comments='#',
is_full=False,
is_out=False):
"""
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
:param is_out:
:param fname: file with data
:param dtype: You should define the colums: time, mag, err and filter,
example: (('time', '<f4'), ('filter', 'S1'), ('mag', '<f4'), ('err', '<f4'))
:param skiprows: skip rows, default: 1 for header
:param comments: skip comments, default: #
:param is_full: return also table data, default: False
:param is_out: print first line of data
:return: curves
"""
from pystella.rf import band
band.Band.load_settings()
if dtype is None:
dtype = [('time', np.float), ('filter', 'S8'), ('mag', np.float),
('err', np.float)]
lc_data = np.loadtxt(fname,
skiprows=skiprows,
dtype=dtype,
comments=comments) # jd filter mag mage
if is_out:
print(lc_data.dtype)
print(lc_data[0])
print(lc_data[1])
b_tot = lc_data['filter']
bnames = np.unique(b_tot)
curves = SetLightCurve()
for bname in bnames:
bname_s = bname
try:
bname_s = bname_s.decode()
except AttributeError:
pass
if band.is_exist(bname_s):
# filter of the current band
is_good = np.array(list(map(lambda x: x == bname, b_tot)),
dtype=bool)
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_s)
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))
if is_full:
return curves, lc_data
return curves
def main(name='', path='./'):
model_ext = '.ph'
is_time_points = False
z = 0
distance = 10. # pc
band.Band.load_settings()
try:
opts, args = getopt.getopt(sys.argv[1:], "hwtp:i:b:")
except getopt.GetoptError as err:
print(str(err)) # will print something like "option -a not recognized"
usage()
sys.exit(2)
if not name:
if len(opts) == 0:
usage()
sys.exit(2)
for opt, arg in opts:
if opt == '-i':
path = ROOT_DIRECTORY
name = str(arg)
break
bands = ['UVW1', 'U']
for opt, arg in opts:
if opt == '-b':
bands = str(arg).split('-')
for b in bands:
if not band.is_exist(b):
print('No such band: ' + b)
sys.exit(2)
elif opt == '-p':
path = os.path.expanduser(str(arg))
if not (os.path.isdir(path) and os.path.exists(path)):
print("No such directory: " + path)
sys.exit(2)
elif opt == '-t':
is_time_points = True
elif opt == '-h':
usage()
sys.exit(2)
names = []
if name != '':
names.append(name)
else: # run for all files in the path
files = [
f for f in os.listdir(path)
if isfile(join(path, f)) and f.endswith(model_ext)
]
for f in files:
names.append(os.path.splitext(f)[0])
if len(names) > 0:
dic_results = {} # dict((k, None) for k in names)
i = 0
for name in names:
i += 1
mags = compute_mag(name,
path,
bands,
z=z,
distance=distance,
t_cut=0.1,
t_up=5.,
tdiff=0.5)
dmdt = compute_dmdt(mags, bands, is_spline=True, s=0.)
dic_results[name] = dict(m=mags, d=dmdt)
print("Finish: %s [%d/%d]" % (name, i, len(names)))
plot_dmdt(dic_results, bands, is_time_points=is_time_points)
else:
print("There are no models in the directory: %s with extension: %s " %
(path, model_ext))
def main():
view_opts = ('single', 'grid', 'gridl', 'gridm')
opt_grid = view_opts[0]
label = None
fsave = None
callback = None
xlim = None
ylim = None
band.Band.load_settings()
try:
opts, args = getopt.getopt(sys.argv[1:], "hqc:g:b:l:s:x:y:")
except getopt.GetoptError as err:
print(str(err)) # will print something like "option -a not recognized"
usage()
sys.exit(2)
if len(opts) == 0:
usage()
sys.exit(2)
bnames = None
# bnames = ['U', 'B', 'V', 'R', "I"]
# bands = ['U', 'B', 'V', 'R', "I", 'UVM2', "UVW1", "UVW2", 'g', "r", "i"]
for opt, arg in opts:
if opt == '-b':
bnames = []
for b in str(arg).split('-'):
# extract band shift
if ':' in b:
bname, shift = b.split(':')
bshift = {}
if '_' in shift:
bshift[bname] = -float(shift.replace('_', ''))
else:
bshift[bname] = float(shift)
else:
bname = b
if not band.is_exist(bname):
print('No such band: ' + bname)
sys.exit(2)
bnames.append(bname)
continue
if opt == '-c':
c = cb.lc_wrapper(str(arg))
if callback is not None:
c = cb.CallBackArray((callback, c))
callback = c
continue
if opt == '-g':
opt_grid = str.strip(arg).lower()
if opt_grid not in view_opts:
print('No such view option: {0}. Can be '.format(opt_grid, '|'.join(view_opts)))
sys.exit(2)
continue
if opt == '-l':
label = str.strip(arg)
continue
if opt == '-s':
fsave = str.strip(arg)
continue
if opt == '-x':
xlim = list(float(x) for x in str(arg).split(':'))
continue
if opt == '-y':
ylim = list(float(x) for x in str(arg).split(':'))
continue
elif opt == '-h':
usage()
sys.exit(2)
if callback is None:
print('No obs data. You my use lcobs or other callbacks.')
usage()
sys.exit(2)
if opt_grid in view_opts[1:]:
sep = opt_grid[:-1]
if sep == 'd':
sep = 'l' # line separator
fig = plot_grid(callback, bnames, xlim=xlim, ylim=ylim, sep=sep, is_grid=False)
else:
fig = plot_all(callback, bnames, xlim=xlim, ylim=ylim, title=label)
plt.show()
# plt.show(block=False)
if fsave is not None:
if fsave == 1:
fsave = "ubv_obs"
d = os.path.expanduser('~/')
fsave = os.path.join(d, os.path.splitext(fsave)[0]) + '.pdf'
print("Save plot to %s " % fsave)
fig.savefig(fsave, bbox_inches='tight')