def test_row_tuple_column_slice():
"""
Test getting and setting a row using a tuple or list of column names
"""
t = table.QTable([[1, 2, 3] * u.m,
[10., 20., 30.],
[100., 200., 300.],
['x', 'y', 'z']], names=['a', 'b', 'c', 'd'])
# Get a row for index=1
r1 = t[1]
# Column slice with tuple of col names
r1_abc = r1['a', 'b', 'c'] # Row object for these cols
r1_abc_repr = ['<Row index=1>',
' a b c ',
' m ',
'float64 float64 float64',
'------- ------- -------',
' 2.0 20.0 200.0']
assert repr(r1_abc).splitlines() == r1_abc_repr
# Column slice with list of col names
r1_abc = r1[['a', 'b', 'c']]
assert repr(r1_abc).splitlines() == r1_abc_repr
# Make sure setting on a tuple or slice updates parent table and row
r1['c'] = 1000
r1['a', 'b'] = 1000 * u.cm, 100.
assert r1['a'] == 10 * u.m
assert r1['b'] == 100
assert t['a'][1] == 10 * u.m
assert t['b'][1] == 100.
assert t['c'][1] == 1000
# Same but using a list of column names instead of tuple
r1[['a', 'b']] = 2000 * u.cm, 200.
assert r1['a'] == 20 * u.m
assert r1['b'] == 200
assert t['a'][1] == 20 * u.m
assert t['b'][1] == 200.
# Set column slice of column slice
r1_abc['a', 'c'] = -1 * u.m, -10
assert t['a'][1] == -1 * u.m
assert t['b'][1] == 200.
assert t['c'][1] == -10.
# Bad column name
with pytest.raises(KeyError) as err:
t[1]['a', 'not_there']
assert "'not_there'" in str(err.value)
# Too many values
with pytest.raises(ValueError) as err:
t[1]['a', 'b'] = 1 * u.m, 2, 3
assert 'right hand side must be a sequence' in str(err.value)
# Something without a length
with pytest.raises(ValueError) as err:
t[1]['a', 'b'] = 1
assert 'right hand side must be a sequence' in str(err.value)
def test_validate_write_kwargs():
out = StringIO()
t = table.QTable([[1, 2], [1, 2]], names=['a', 'b'])
with pytest.raises(TypeError, match=r"write\(\) argument 'fast_writer' must be a "
r"\(<class 'bool'>, <class 'str'>\) object, "
r"got <class 'int'> instead"):
ascii.write(t, out, fast_writer=12)
def photometry_to_table(
self,
output: str = None,
best: bool = False,
fmts: List[str] = ("ascii.ecsv", "ascii.csv")
):
"""
Converts the photometry information, which is stored internally as a dictionary, into an astropy QTable.
:param output: Where to write table.
:return:
"""
if output is None:
output = self.build_photometry_table_path()
# if self.photometry_tbl is None:
tbls = []
for instrument_name in self.photometry:
instrument = inst.Instrument.from_params(instrument_name)
for filter_name in self.photometry[instrument_name]:
fil = instrument.filters[filter_name]
if best:
phot_dict, _ = self.select_photometry_sep(fil=filter_name, instrument=instrument_name)
phot_dict["band"] = filter_name
phot_dict["instrument"] = instrument_name
phot_dict["lambda_eff"] = u.check_quantity(
number=fil.lambda_eff,
unit=units.Angstrom
)
# tbl = table.QTable([phot_dict])
tbls.append(phot_dict)
print("phot_dict:")
print(phot_dict)
else:
for epoch in self.photometry[instrument_name][filter_name]:
phot_dict = self.photometry[instrument_name][filter_name][epoch].copy()
phot_dict["band"] = filter_name
phot_dict["instrument"] = instrument_name
phot_dict["lambda_eff"] = u.check_quantity(
number=fil.lambda_eff,
unit=units.Angstrom
)
# tbl = table.QTable([phot_dict])
tbls.append(phot_dict)
print(tbls)
if best:
self.photometry_tbl = table.vstack(tbls)
else:
self.photometry_tbl = table.QTable(tbls)
if output is not False:
for fmt in fmts:
self.photometry_tbl.write(output.replace(".ecsv", fmt[fmt.find("."):]), format=fmt, overwrite=True)
return self.photometry_tbl
def test_write_formatted_mixin(fast_writer):
"""
Test fix for #8680 where writing a QTable with a quantity mixin generates
an exception if a format is specified.
"""
out = StringIO()
t = table.QTable([[1, 2], [1, 2] * u.m], names=['a', 'b'])
ascii.write(t, out, fast_writer=fast_writer, formats={'a': '%02d', 'b': '%.2f'})
assert out.getvalue().splitlines() == ['a b',
'01 1.00',
'02 2.00']
def test_quantity_mixin(tmpdir):
t = table.QTable()
t['a'] = [1, 2, 3]
t['b'] = ['x', 'y', 'z']
t['c'] = [2.0, 5.0, 8.2] * u.m
def check(ff):
assert isinstance(ff['table']['c'], u.Quantity)
helpers.assert_roundtrip_tree({'table': t}, tmpdir, asdf_check_func=check)
def __init__(self,
name='SED Catalog',
marker='circle',
color='blue',
verbose=True,
**kwargs):
"""Initialize the Catalog object"""
# Metadata
self.verbose = verbose
self.name = name
self.marker = marker
self.color = color
self.wave_units = q.um
self.flux_units = q.erg / q.s / q.cm**2 / q.AA
# List all the results columns
self.cols = [
'name', 'age', 'age_unc', 'distance', 'distance_unc', 'parallax',
'parallax_unc', 'radius', 'radius_unc', 'spectral_type',
'spectral_type_unc', 'SpT', 'SpT_fit', 'membership', 'reddening',
'fbol', 'fbol_unc', 'mbol', 'mbol_unc', 'Lbol', 'Lbol_unc',
'Lbol_sun', 'Lbol_sun_unc', 'Mbol', 'Mbol_unc', 'logg', 'logg_unc',
'mass', 'mass_unc', 'Teff', 'Teff_unc', 'Teff_evo', 'Teff_evo_unc',
'Teff_bb', 'SED'
]
# A master table of all SED results
self.results = at.QTable(names=self.cols, dtype=['O'] * len(self.cols))
self.results.add_index('name')
# Set the units
self.results['age'].unit = q.Gyr
self.results['age_unc'].unit = q.Gyr
self.results['distance'].unit = q.pc
self.results['distance_unc'].unit = q.pc
self.results['parallax'].unit = q.mas
self.results['parallax_unc'].unit = q.mas
self.results['radius'].unit = q.Rsun
self.results['radius_unc'].unit = q.Rsun
self.results['fbol'].unit = q.erg / q.s / q.cm**2
self.results['fbol_unc'].unit = q.erg / q.s / q.cm**2
self.results['Lbol'].unit = q.erg / q.s
self.results['Lbol_unc'].unit = q.erg / q.s
self.results['mass'].unit = q.Msun
self.results['mass_unc'].unit = q.Msun
self.results['Teff'].unit = q.K
self.results['Teff_unc'].unit = q.K
self.results['Teff_bb'].unit = q.K
self.results['Teff_evo'].unit = q.K
self.results['Teff_evo_unc'].unit = q.K
# Try to set attributes from kwargs
for k, v in kwargs.items():
setattr(self, k, v)
def test_column_value_access():
"""Can a column's underlying data consistently be accessed via `.value`,
whether it is a `Column`, `MaskedColumn`, `Quantity`, or `Time`?"""
data = np.array([1, 2, 3])
tbl = table.QTable({'a': table.Column(data),
'b': table.MaskedColumn(data),
'c': u.Quantity(data),
'd': time.Time(data, format='mjd')})
assert type(tbl['a'].value) == np.ndarray
assert type(tbl['b'].value) == np.ma.MaskedArray
assert type(tbl['c'].value) == np.ndarray
assert type(tbl['d'].value) == np.ndarray
def test_row_tuple_column_slice_transaction():
"""
Test that setting a row that fails part way through does not
change the table at all.
"""
t = table.QTable([[10., 20., 30.], [1, 2, 3] * u.m], names=['a', 'b'])
tc = t.copy()
# First one succeeds but second fails.
with pytest.raises(ValueError) as err:
t[1]['a', 'b'] = (-1, -1 * u.s) # Bad unit
assert "'s' (time) and 'm' (length) are not convertible" in str(err.value)
assert t[1] == tc[1]
def aggregate_one(res_fname, mlband):
with read_results.PCAOutput.from_fname(res_fname) as res:
with res.get_drp_logcube(mpl_v) as drp, res.get_dap_maps(mpl_v, daptype) as dap:
plateifu = res[0].header['PLATEIFU']
plate, ifu = plateifu.split('-')
stellarmass = totalmass.StellarMass(
res, pca_system, drp, dap, drpall.loc[plateifu],
cosmo, mlband=mlband)
mstar_map = stellarmass.mstar[stellarmass.bands_ixs[mlband], ...]
tauVmu_med = res.param_dist_med('tau_V mu')
tauV1mmu_med = res.param_dist_med('tau_V (1 - mu)')
tauV_med = tauVmu_med + tauV1mmu_med
mean_atten_mwtd = np.average(
tauV_med, weights=(mstar_map * ~res.mask))
std_atten_mwtd = np.sqrt(np.average(
(tauV_med - mean_atten_mwtd)**2., weights=(mstar_map * ~res.mask)))
mass_in_ifu = stellarmass.mstar_in_ifu[stellarmass.bands_ixs[stellarmass.mlband]]
sollum_in_ifu = stellarmass.sollum_bands.to(m.bandpass_sol_l_unit).sum(axis=(1, 2))
sollum_nsa = stellarmass.nsa_absmags_cosmocorr.to(
m.bandpass_sol_l_unit,
totalmass.bandpass_flux_to_solarunits(stellarmass.absmag_sun))
ml_fluxwt = stellarmass.logml_fnuwt
outerml_ring = stellarmass.ml_ring()
sollum_nsa_names = list(map(
lambda n: 'sollum_nsa_{}'.format(n),
stellarmass.bands))
sollum_in_ifu_names = list(map(
lambda n: 'sollum_in_ifu_{}'.format(n),
stellarmass.bands))
data = [plateifu, mean_atten_mwtd, std_atten_mwtd,
mass_in_ifu, *sollum_in_ifu, *sollum_nsa,
ml_fluxwt.to(m.m_to_l_unit), outerml_ring.to(m.m_to_l_unit)]
names = ['plateifu', 'mean_atten_mwtd' ,'std_atten_mwtd',
'mass_in_ifu', *sollum_in_ifu_names, *sollum_nsa_names,
'ml_fluxwt', 'outerml_ring']
qt = t.QTable()
for d, n in zip(data, names):
qt[n] = np.atleast_1d(d)
return qt
def from_tree(cls, node, ctx):
# This is getting meta, guys
meta = node.get('meta', {})
# This enables us to support files that use the table definition from
# the ASDF Standard, rather than the custom one that Astropy defines.
if cls._compat:
return table.Table(node['columns'], meta=meta)
if node.get('qtable', False):
t = table.QTable(meta=node.get('meta', {}))
else:
t = table.Table(meta=node.get('meta', {}))
for name, col in zip(node['colnames'], node['columns']):
t[name] = col
return t
def get_nearest_calib_rows(self, mjd: float, n: int = 7):
# self.retrieve_calibration_table()
row_prime = self.get_nearest_calib_row(mjd=mjd)
rows = [row_prime]
mjd_low = mjd - 1
mjd_high = mjd + 1
while len(rows) < n:
row = self.get_nearest_calib_row(mjd=mjd_high)
if row not in rows:
rows.append(row)
row = self.get_nearest_calib_row(mjd=mjd_low)
if row not in rows:
rows.append(row)
# print(mjd_low, mjd_high)
mjd_low -= 1
mjd_high += 1
tbl = table.QTable(rows=rows, names=rows[0].colnames)
tbl.sort("mjd_obs")
return tbl
def to_table(self):
'''
make table of stellar-mass results
'''
tab = t.QTable()
tab['plateifu'] = [self.drpall_row['plateifu']]
# tabulate mass in IFU
tab['mass_in_ifu'] = self.mstar_in_ifu[
None, ...][:, self.bands_ixs[self.mlband]]
nsa_absmag = self.nsa_absmags_cosmocorr
#tab['nsa_absmag'].meta['bands'] = self.bands
ifu_absmag = (self.ifu_flux_bands.to(u.ABmag) - self.distmod)
#tab['ifu_absmag'].meta['bands'] = self.bands
missing_flux = ((nsa_absmag + self.distmod).to(m.Mgy) -
(ifu_absmag + self.distmod).to(m.Mgy)).clip(
a_min=0. * m.Mgy, a_max=np.inf * m.Mgy)
for i, b in enumerate(self.bands):
outer_flux = missing_flux[i]
if outer_flux <= 0. * m.Mgy:
tab['outer_absmag_{}'.format(b)] = np.inf * u.ABmag
tab['outer_lum_{}'.format(b)] = -np.inf * u.dex(
m.bandpass_sol_l_unit)
else:
tab['outer_absmag_{}'.format(b)] = outer_flux.to(
u.ABmag) - self.distmod
tab['outer_lum_{}'.format(b)] = tab['outer_absmag_{}'.format(
b)].to(
u.dex(m.bandpass_sol_l_unit),
bandpass_flux_to_solarunits(StellarMass.absmag_sun[i]))
tab['outer_ml_ring'] = self.ml_ring()
#tab['outer_ml_ring'].meta['band'] = self.mlband
tab['ml_fluxwt'] = self.logml_fnuwt
#tab['ml_fluxwt'].meta['band'] = self.mlband
tab['distmod'] = self.distmod[None, ...]
return tab
def test_qtable_column_conversion():
"""
Ensures that a QTable that gets assigned a unit switches to be Quantity-y
"""
qtab = table.QTable([[1, 2], [3, 4.2]], names=['i', 'f'])
assert isinstance(qtab['i'], table.column.Column)
assert isinstance(qtab['f'], table.column.Column)
qtab['i'].unit = 'km/s'
assert isinstance(qtab['i'], u.Quantity)
assert isinstance(qtab['f'], table.column.Column)
# should follow from the above, but good to make sure as a #4497 regression test
assert isinstance(qtab['i'][0], u.Quantity)
assert isinstance(qtab[0]['i'], u.Quantity)
assert not isinstance(qtab['f'][0], u.Quantity)
assert not isinstance(qtab[0]['f'], u.Quantity)
# Regression test for #5342: if a function unit is assigned, the column
# should become the appropriate FunctionQuantity subclass.
qtab['f'].unit = u.dex(u.cm / u.s**2)
assert isinstance(qtab['f'], u.Dex)
def load_master_table(
tbl: Union[None, table.Table],
tbl_columns: dict,
tbl_path: str,
force: bool = False,
):
if force or tbl is None:
colnames, dtypes, un = _construct_column_lists(columns=tbl_columns)
if not os.path.isfile(tbl_path):
tbl = table.QTable(data=[[-999]] * len(colnames),
names=colnames,
units=un,
dtype=dtypes)
for i, colname in enumerate(colnames):
print(i, colname)
if isinstance(dtypes[i], str):
tbl[colname][0] = "0" * 32
tbl.write(tbl_path, format="ascii.ecsv")
tbl = table.QTable.read(tbl_path, format="ascii.ecsv")
for i, colname in enumerate(colnames):
add_column(tbl=tbl, colname=colname, dtype=dtypes[i], unit=un[i])
return tbl
def main(gammafile, protonfile, electronfile, outputfile):
logging.basicConfig(level=logging.INFO)
logging.getLogger("pyirf").setLevel(logging.DEBUG)
particles = {
"gamma": {
"file": gammafile,
"target_spectrum": CRAB_HEGRA,
},
"proton": {
"file": protonfile,
"target_spectrum": IRFDOC_PROTON_SPECTRUM,
},
"electron": {
"file": electronfile,
"target_spectrum": IRFDOC_ELECTRON_SPECTRUM,
},
}
for particle_type, p in particles.items():
log.info(f"Simulated {particle_type.title()} Events:")
p["events"], p["simulation_info"] = read_file(p["file"])
p["events"]["particle_type"] = particle_type
p["simulated_spectrum"] = PowerLaw.from_simulation(
p["simulation_info"], T_OBS)
p["events"]["weight"] = calculate_event_weights(
p["events"]["true_energy"], p["target_spectrum"],
p["simulated_spectrum"])
for prefix in ('true', 'reco'):
k = f"{prefix}_source_fov_offset"
p["events"][k] = calculate_source_fov_offset(p["events"],
prefix=prefix)
log.info(p["simulation_info"])
log.info("")
gammas = particles["gamma"]["events"]
background = table.vstack(
[particles["proton"]["events"], particles["electron"]["events"]])
# calculate theta / distance between reco and assuemd source position
gammas["theta"] = calculate_theta(
gammas,
assumed_source_az=gammas["true_az"],
assumed_source_alt=gammas["true_alt"],
)
INITIAL_GH_CUT = np.quantile(gammas['gh_score'],
(1 - INITIAL_GH_CUT_EFFICENCY))
log.info(
f"Using fixed G/H cut of {INITIAL_GH_CUT} to calculate theta cuts")
theta_bins = add_overflow_bins(
create_bins_per_decade(10**-1.8 * u.TeV,
10**2.41 * u.TeV,
bins_per_decade=25))
sensitivity_bins = add_overflow_bins(
create_bins_per_decade(10**-1.8 * u.TeV,
10**2.41 * u.TeV,
bins_per_decade=5))
# theta cut is 68 percent containmente of the gammas
# for now with a fixed global, unoptimized score cut
mask_theta_cuts = gammas["gh_score"] >= INITIAL_GH_CUT
theta_cuts = calculate_percentile_cut(
gammas["theta"][mask_theta_cuts],
gammas["reco_energy"][mask_theta_cuts],
bins=theta_bins,
min_value=0.05 * u.deg,
fill_value=0.32 * u.deg,
max_value=0.32 * u.deg,
percentile=68,
)
log.info("Optimizing G/H separation cut for best sensitivity")
gh_cut_efficiencies = np.arange(
GH_CUT_EFFICIENCY_STEP,
MAX_GH_CUT_EFFICIENCY + GH_CUT_EFFICIENCY_STEP / 2,
GH_CUT_EFFICIENCY_STEP)
sensitivity_step_2, gh_cuts = optimize_gh_cut(
gammas,
background,
reco_energy_bins=sensitivity_bins,
gh_cut_efficiencies=gh_cut_efficiencies,
op=operator.ge,
theta_cuts=theta_cuts,
alpha=ALPHA,
background_radius=MAX_BG_RADIUS,
)
# now that we have the optimized gh cuts, we recalculate the theta
# cut as 68 percent containment on the events surviving these cuts.
log.info('Recalculating theta cut for optimized GH Cuts')
for tab in (gammas, background):
tab["selected_gh"] = evaluate_binned_cut(tab["gh_score"],
tab["reco_energy"], gh_cuts,
operator.ge)
theta_cuts_opt = calculate_percentile_cut(
gammas[gammas['selected_gh']]["theta"],
gammas[gammas['selected_gh']]["reco_energy"],
theta_bins,
percentile=68,
fill_value=0.32 * u.deg,
max_value=0.32 * u.deg,
min_value=0.05 * u.deg,
)
gammas["selected_theta"] = evaluate_binned_cut(gammas["theta"],
gammas["reco_energy"],
theta_cuts_opt, operator.le)
gammas["selected"] = gammas["selected_theta"] & gammas["selected_gh"]
# calculate sensitivity
signal_hist = create_histogram_table(gammas[gammas["selected"]],
bins=sensitivity_bins)
background_hist = estimate_background(
background[background["selected_gh"]],
reco_energy_bins=sensitivity_bins,
theta_cuts=theta_cuts_opt,
alpha=ALPHA,
background_radius=MAX_BG_RADIUS,
)
sensitivity = calculate_sensitivity(signal_hist,
background_hist,
alpha=ALPHA)
# scale relative sensitivity by Crab flux to get the flux sensitivity
spectrum = particles['gamma']['target_spectrum']
for s in (sensitivity_step_2, sensitivity):
s["flux_sensitivity"] = (s["relative_sensitivity"] *
spectrum(s['reco_energy_center']))
hdus = [
fits.PrimaryHDU(),
fits.BinTableHDU(sensitivity, name="SENSITIVITY"),
fits.BinTableHDU(sensitivity_step_2, name="SENSITIVITY_STEP_2"),
fits.BinTableHDU(theta_cuts, name="THETA_CUTS"),
fits.BinTableHDU(theta_cuts_opt, name="THETA_CUTS_OPT"),
fits.BinTableHDU(gh_cuts, name="GH_CUTS"),
]
# calculate sensitivity using unoptimised cuts
gammas["theta_unop"] = gammas["theta"].to_value(u.deg) <= np.sqrt(0.03)
gammas["gh_unop"] = gammas["gh_score"] > 0.85
theta_cut_unop = table.QTable()
theta_cut_unop['low'] = theta_cuts_opt['low']
theta_cut_unop['high'] = theta_cuts_opt['high']
theta_cut_unop['center'] = theta_cuts_opt['center']
theta_cut_unop['cut'] = np.sqrt(0.03) * u.deg
signal_hist_unop = create_histogram_table(gammas[gammas["theta_unop"]
& gammas["gh_unop"]],
bins=sensitivity_bins)
background_hist_unop = estimate_background(
background[background["gh_score"] > 0.85],
reco_energy_bins=sensitivity_bins,
theta_cuts=theta_cut_unop,
alpha=ALPHA,
background_radius=MAX_BG_RADIUS,
)
sensitivity_unop = calculate_sensitivity(signal_hist_unop,
background_hist_unop,
alpha=ALPHA)
sensitivity_unop["flux_sensitivity"] = (
sensitivity_unop["relative_sensitivity"] *
spectrum(sensitivity_unop['reco_energy_center']))
hdus.append(fits.BinTableHDU(sensitivity_unop, name="SENSITIVITY_UNOP"))
log.info('Calculating IRFs')
masks = {
"": gammas["selected"],
"_NO_CUTS": slice(None),
"_ONLY_GH": gammas["selected_gh"],
"_ONLY_THETA": gammas["selected_theta"],
}
# binnings for the irfs
true_energy_bins = add_overflow_bins(
create_bins_per_decade(10**-1.8 * u.TeV,
10**2.41 * u.TeV,
bins_per_decade=10))
reco_energy_bins = add_overflow_bins(
create_bins_per_decade(10**-1.8 * u.TeV,
10**2.41 * u.TeV,
bins_per_decade=5))
fov_offset_bins = [0, 0.5] * u.deg
source_offset_bins = np.arange(0, 1 + 1e-4, 1e-3) * u.deg
energy_migration_bins = np.geomspace(0.2, 5, 200)
for label, mask in masks.items():
effective_area = effective_area_per_energy(
gammas[mask],
particles["gamma"]["simulation_info"],
true_energy_bins=true_energy_bins,
)
hdus.append(
create_aeff2d_hdu(
effective_area[...,
np.newaxis], # add one dimension for FOV offset
true_energy_bins,
fov_offset_bins,
extname="EFFECTIVE_AREA" + label,
))
edisp = energy_dispersion(
gammas[mask],
true_energy_bins=true_energy_bins,
fov_offset_bins=fov_offset_bins,
migration_bins=energy_migration_bins,
)
hdus.append(
create_energy_dispersion_hdu(
edisp,
true_energy_bins=true_energy_bins,
migration_bins=energy_migration_bins,
fov_offset_bins=fov_offset_bins,
extname="ENERGY_DISPERSION" + label,
))
bias_resolution = energy_bias_resolution(
gammas[gammas["selected"]],
true_energy_bins,
)
ang_res = angular_resolution(
gammas[gammas["selected_gh"]],
true_energy_bins,
)
psf = psf_table(
gammas[gammas["selected_gh"]],
true_energy_bins,
fov_offset_bins=fov_offset_bins,
source_offset_bins=source_offset_bins,
)
background_rate = background_2d(
background[background['selected_gh']],
reco_energy_bins,
fov_offset_bins=np.arange(0, 11) * u.deg,
t_obs=T_OBS,
)
hdus.append(
create_background_2d_hdu(
background_rate,
reco_energy_bins,
fov_offset_bins=np.arange(0, 11) * u.deg,
))
hdus.append(
create_psf_table_hdu(
psf,
true_energy_bins,
source_offset_bins,
fov_offset_bins,
))
hdus.append(
create_rad_max_hdu(theta_cuts_opt["cut"][:, np.newaxis], theta_bins,
fov_offset_bins))
hdus.append(fits.BinTableHDU(ang_res, name="ANGULAR_RESOLUTION"))
hdus.append(
fits.BinTableHDU(bias_resolution, name="ENERGY_BIAS_RESOLUTION"))
log.info('Writing outputfile')
fits.HDUList(hdus).writeto(outputfile, overwrite=True)
def generate_data(path=resource_filename('locals', 'data/fake/'),
mag_range=(11.13, 18)):
"""Generate a fake JWST pipeline catalog replete with photometry and spectra
using a range of model atmospheres
Parameters
----------
path: str
The path to the target directory
"""
# Get some random spectra
try:
files = glob.glob('/user/jfilippazzo/Models/ACES/default/*.fits')[::50]
except:
files = glob.glob(
'/Users/jfilippazzo/Documents/Modules/_DEPRECATED/limb_dark_jeff/limb/specint/*.fits'
)[::20]
# Make a fake source catalog (with only essential columns for now)
catpath = os.path.join(path, 'fake_source_catalog.ecsv')
ids = list(range(len(files)))
coords = SkyCoord([89.7455] * len(ids), [-29.05744] * len(ids),
unit='deg',
frame='icrs')
cat = at.QTable([ids, coords], names=('id', 'icrs_centroid'))
cat.write(catpath)
# Open the x1d file
header = fits.getheader(
resource_filename('locals', 'data/template_x1d.fits'))
# Make Spectrum objects from models at R=150
wavelength = np.arange(0.05, 2.6, 0.0001)[::66] * q.um
# Normalize the spectra to a random F200W magnitude
spectra = []
f200w = Bandpass('NIRISS.F200W')
f200w.wave_units = q.um
for file in files:
# Create Spectrum
flux = fits.getdata(file)[-1][::66] * q.erg / q.s / q.cm**2 / q.AA
unc = flux / 50.
spec = Spectrum(wavelength, flux, unc)
# Normalize to F200W
mag = np.random.uniform(*mag_range)
norm_spec = spec.renormalize(mag, f200w)
spectra.append(norm_spec)
# Make a separate x1d file and photometry file for each bandpass
# containing data for each source
for band in NIRISS_bands:
try:
# Get the Bandpass object
bp = Bandpass(band)
bp.wave_units = q.um
# Make x1d file for spectra
x1d_file = os.path.join(path, '{}_x1d.fits'.format(band))
x1d_hdu = fits.HDUList(fits.PrimaryHDU(header=header))
# Make csv file for photometry
phot_file = os.path.join(path, '{}_phot.csv'.format(band))
phot_data = at.Table(names=('id', 'band', 'magnitude',
'magnitude_unc'),
dtype=(int, 'S20', float, float))
# Iterate over spectra
for id, (f, spec) in enumerate(zip(files, spectra)):
# Trim spectrum to bandpass for x1d file
spec = Spectrum(*spec.spectrum,
trim=[
(0 * q.um, bp.WavelengthMin * 1E-4 * q.um),
(bp.WavelengthMax * 1E-4 * q.um, 10 * q.um)
])
# Calculate magnitude and add to photometry table
mag, mag_unc = spec.synthetic_magnitude(bp, force=True)
phot_data.add_row([id, band, mag, mag_unc])
# Add source spectrum params for verification
params = f.split('/')[-1].split('-')
header['TEFF'] = int(params[0].replace('lte', ''))
header['LOGG'] = float(params[1][:4])
header['FEH'] = float(params[-6][:-8].split('+')[-1])
header['FILEPATH'] = f
header['PUPIL'] = band
# Put spectrum in x1d fits file
data = fits.BinTableHDU(data=np.rec.array(
list(zip(*spec.data)),
formats='float32,float32,float32',
names='WAVELENGTH,FLUX,ERROR'),
header=header)
data.name = 'EXTRACT1D'
x1d_hdu.append(data)
# Write the photometry file
phot_data.write(phot_file, format='ascii.csv')
del phot_data
# Write the x1d file
x1d_hdu.writeto(x1d_file, overwrite=True)
del x1d_hdu
except IOError:
pass
ax.set_ylabel("temperature")
ax.set_title(f"ch #{ch}")
ax.legend()
fig.tight_layout()
fig.savefig(output_dir / f"temp_vs_subrefz.{image_format}")
if do_plot:
plt.show()
else:
plt.clf()
plt.close()
# 4th step: Gauss-fit
print("#4: Gauss-fit")
alldata = table.QTable(names=("scan_speed", "peak", "z_mean", "z_stddev",
"slope", "intercept"))
if maxid[0] < minid[0]:
minid.insert(0, np.nan)
if minid[-1] < maxid[-1]:
minid.append(np.nan)
amp0 = params["fitting"]["amplitude"]
z0 = params["fitting"]["z_mean"]
s0 = params["fitting"]["z_stddev"]
sl = params["fitting"]["slope"]
ic = params["fitting"]["intercept"]
g_init = models.Gaussian1D(amplitude=amp0, mean=z0,
stddev=s0) + models.Linear1D(sl, ic)
fit_g = fitting.LevMarLSQFitter()
mask[exchs] = False
mask[np.where(scanarray_cal.kidtp != 1)] = False
masked_cube_array = cube_array[:, :, mask]
weight = dc.ones_like(masked_cube_array)
cont_array = fc.makecontinuum(masked_cube_array, weight=weight)
dc.io.savefits(cont_array, cont_obs_fits, dropdeg=True, overwrite=True)
# 5th step: 2D-Gauss fit on the continuum map
print("#5: 2D-Gauss fit on the continuum map")
alldata = table.QTable(names=(
"subref_x",
"subref_y",
"peak",
"x_mean",
"y_mean",
"x_stddev",
"y_stddev",
"theta",
))
amplitude = float(cont_array.max().values)
x_mean = float(
cont_array.where(cont_array == cont_array.max(), drop=True).x.values)
y_mean = float(
cont_array.where(cont_array == cont_array.max(), drop=True).y.values)
x_stddev = params["fitting"]["x_stddev"]
y_stddev = params["fitting"]["y_stddev"]
theta = params["fitting"]["theta"]
f = fc.gauss_fit(
def into_pixels(xdata,
ydata,
nx=None,
ny=None,
xscale=None,
yscale=None,
xlim=None,
ylim=None,
x="x",
y="y",
id="id",
n="N",
quiet=False):
"""
Put a 2D dataset into pixels. The code returns two objects:
1) an astropy QTable for the pixels with the pixel ID number, x-centre,
y-centre, and number of objects -- the properties of the pixel grid
are also output in the Qtable metadata;
2) an array containing the pixel ID number of all input objects --
objects outside the limits of the pixel grid are given a pixel ID of -1.
INPUTS
xdata : first coordinate of data (refered to as "x")
ydata : second coordinate of data (refered to as "y")
OPTIONS
nx : number of pixels in x [default None] (*)
ny : number of pixels in y [default None] (*)
xscale : scale of x pixels [default None] (*)
yscale : scale of y pixels [default None] (*)
xlim : limits of pixelised area in x [default None] (*)
ylim : limits of pixelised area in y [default None] (*)
x : name for x-coordinate column of output table [default "x"]
y : name for y-coordinate column of output table [default "y"]
id : name for pixel ID column of output table [default "id"]
n : name for number of datapoints column of output table [default "N"]
quiet : suppress text outputs? [default False]
NOTES
(*) Some pixels settings must be provided, but it is not necessary to
provide all options. The behaviour of the code for different
combinations of inputs is outlined here:
1) No settings are provided: the code will fail.
2) Limits only: the code will fail.
3) Number of pixels only: the data limits are used for the pixel
limits. Then the behaviour follows from case 5.
4) Scale only: the data limits are used but with the lower limit
rounded down to the nearest scale factor and the upper limit
rounded up to the nearest scale factor. Then the behaviour follows
from case 7.
5) Limits and number of pixels: scale is calculated. Then the
behaviour follows from case 8.
6) Scale and number of pixels: limits are chosen so that the centre
of the pixel grid coincides with the centre of the data. Then the
behaviour follows from case 8.
7) Limits and scale: number of pixels is calculated. Then the
behaviour proceeds as case 8.
8) Number of pixels, pixel scale and limits are all given: the code
checks that they are all consistent, and fails if not.
"""
# throw an error if no settings are given for the x pixels
if not xlim and not xscale and not nx:
print("ERROR: Please provide pixel settings for the x-coordinate.")
return
# throw an error if no settings are given for the y pixels
if not ylim and not yscale and not ny:
print("ERROR: Please provide pixel settings for the y-coordinate.")
return
# do no proceed if only limits are given for x-coordinate
if xlim and not xscale and not nx:
print("ERROR: Please provide required number of pixels or pixel "\
+"scale for x-coordinate as well as limits of pixelised region.")
return
# do no proceed if only limits are given for y-coordinate
if ylim and not yscale and not ny:
print("ERROR: Please provide required number of pixels or pixel "\
+"scale for y-coordinate as well as limits of pixelised region.")
return
# calculate limits, if needed
if not xlim:
if nx and xscale:
xmid = xdata.min() + xdata.ptp() / 2.
xlim = (xmid - nx / 2. * xscale, xmid + nx / 2. * xscale)
elif not xscale:
xlim = (xdata.min(), xdata.max())
else:
xlim = (np.floor(xdata.min() / xscale) * xscale,
np.ceil(xdata.max() / xscale) * xscale)
if not ylim:
if ny and yscale:
ymid = ydata.min() + ydata.ptp() / 2.
ylim = (ymid - ny / 2. * yscale, ymid + ny / 2. * yscale)
elif not yscale:
ylim = (ydata.min(), ydata.max())
else:
ylim = (np.floor(ydata.min() / yscale) * yscale,
np.ceil(ydata.max() / yscale) * yscale)
# calculate pixel scale, if needed
if not xscale: xscale = (xlim[1] - xlim[0]) / nx
if not yscale: yscale = (ylim[1] - ylim[0]) / ny
# calculate number of pixels, if needed
if not nx: nx = int(np.round((xlim[1] - xlim[0]) / xscale))
if not ny: ny = int(np.round((ylim[1] - ylim[0]) / yscale))
# make sure pixel numbers are integers
if nx != int(nx):
print("You have a non-integer number of x pixels.")
return
if ny != int(ny):
print("You have a non-integer number of y pixels.")
return
# total number of pixels
npix = nx * ny
# check that everything is consistent
dx = 1 - (xlim[1] - xlim[0]) / nx / xscale
dy = 1 - (ylim[1] - ylim[0]) / ny / yscale
if np.abs(dx) > 1e-3 or np.abs(dy) > 1e-3:
if np.abs(dx) > 1e-3: print("ERROR: Your x-coordinate scales, limits, "\
+"and pixel numbers are inconsistent.")
if np.abs(dy) > 1e-3: print("ERROR: Your y-coordinate scales, limits, "\
+"and pixel numbers are inconsistent.")
return
if not quiet:
print("\nbin 2D data into pixels")
print("")
print(" x coordinate: {:}".format(x))
print(" y coordinate: {:}".format(y))
print("")
print(" x scale: {:} /pixel".format(xscale))
print(" y scale: {:} /pixel".format(yscale))
print("")
print(" x limits: {:} to {:}".format(*xlim))
print(" y limits: {:} to {:}".format(*ylim))
print("")
print(" x pixels: {:}".format(nx))
print(" y pixels: {:}".format(ny))
print(" total pixels: {:}".format(npix))
# make QTable for pixels
pix = table.QTable()
pix[id] = range(npix)
# pixel centres
xx = np.linspace(xlim[0] / xscale + 0.5, xlim[1] / xscale - 0.5,
nx) * xscale
yy = np.linspace(ylim[0] / yscale + 0.5, ylim[1] / yscale - 0.5,
ny) * yscale
pix[x], pix[y] = [p.reshape(npix) for p in np.meshgrid(xx, yy)]
# pixel number for each datapoint
data_pix = (np.round((xdata-xx.min())/xscale) \
+ np.round((ydata-yy.min())/yscale)*nx).astype(int)
data_pix[(xdata<xlim[0])|(xdata>xlim[1])|(ydata<ylim[0])|(ydata>ylim[1])]\
= -1
# number of datapoints in each pixel
pix[n] = np.histogram(data_pix, range=(-0.5, npix - 0.5), bins=npix)[0]
# put grid properties into metadata
pix.meta = {
"npix": npix,
"nx": nx,
"ny": ny,
"xmin": min(xlim),
"xmax": max(xlim),
"ymin": min(ylim),
"ymax": max(ylim),
"xscale": xscale,
"yscale": yscale,
}
return pix, data_pix
def main():
logging.basicConfig(level=logging.INFO)
logging.getLogger("pyirf").setLevel(logging.DEBUG)
for particle_type, p in particles.items():
log.info(f"Simulated {particle_type.title()} Events:")
p["events"], p["simulation_info"] = read_eventdisplay_fits(p["file"])
p["events"]["particle_type"] = particle_type
p["simulated_spectrum"] = PowerLaw.from_simulation(
p["simulation_info"], T_OBS)
p["events"]["weight"] = calculate_event_weights(
p["events"]["true_energy"], p["target_spectrum"],
p["simulated_spectrum"])
for prefix in ('true', 'reco'):
k = f"{prefix}_source_fov_offset"
p["events"][k] = calculate_source_fov_offset(p["events"],
prefix=prefix)
# calculate theta / distance between reco and assuemd source positoin
# we handle only ON observations here, so the assumed source pos
# is the pointing position
p["events"]["theta"] = calculate_theta(
p["events"],
assumed_source_az=p["events"]["pointing_az"],
assumed_source_alt=p["events"]["pointing_alt"],
)
log.info(p["simulation_info"])
log.info("")
gammas = particles["gamma"]["events"]
# background table composed of both electrons and protons
background = table.vstack(
[particles["proton"]["events"], particles["electron"]["events"]])
INITIAL_GH_CUT = np.quantile(gammas['gh_score'],
(1 - INITIAL_GH_CUT_EFFICENCY))
log.info(
f"Using fixed G/H cut of {INITIAL_GH_CUT} to calculate theta cuts")
# event display uses much finer bins for the theta cut than
# for the sensitivity
theta_bins = add_overflow_bins(
create_bins_per_decade(10**(-1.9) * u.TeV, 10**2.3005 * u.TeV, 50))
# same bins as event display uses
sensitivity_bins = add_overflow_bins(
create_bins_per_decade(10**-1.9 * u.TeV,
10**2.31 * u.TeV,
bins_per_decade=5))
# theta cut is 68 percent containmente of the gammas
# for now with a fixed global, unoptimized score cut
# the cut is calculated in the same bins as the sensitivity,
# but then interpolated to 10x the resolution.
mask_theta_cuts = gammas["gh_score"] >= INITIAL_GH_CUT
theta_cuts_coarse = calculate_percentile_cut(
gammas["theta"][mask_theta_cuts],
gammas["reco_energy"][mask_theta_cuts],
bins=sensitivity_bins,
min_value=0.05 * u.deg,
fill_value=0.32 * u.deg,
max_value=0.32 * u.deg,
percentile=68,
)
# interpolate to 50 bins per decade
theta_center = bin_center(theta_bins)
inter_center = bin_center(sensitivity_bins)
theta_cuts = table.QTable({
"low":
theta_bins[:-1],
"high":
theta_bins[1:],
"center":
theta_center,
"cut":
np.interp(np.log10(theta_center / u.TeV),
np.log10(inter_center / u.TeV), theta_cuts_coarse['cut']),
})
log.info("Optimizing G/H separation cut for best sensitivity")
gh_cut_efficiencies = np.arange(
GH_CUT_EFFICIENCY_STEP,
MAX_GH_CUT_EFFICIENCY + GH_CUT_EFFICIENCY_STEP / 2,
GH_CUT_EFFICIENCY_STEP)
sensitivity, gh_cuts = optimize_gh_cut(
gammas,
background,
reco_energy_bins=sensitivity_bins,
gh_cut_efficiencies=gh_cut_efficiencies,
op=operator.ge,
theta_cuts=theta_cuts,
alpha=ALPHA,
background_radius=MAX_BG_RADIUS,
)
# now that we have the optimized gh cuts, we recalculate the theta
# cut as 68 percent containment on the events surviving these cuts.
log.info('Recalculating theta cut for optimized GH Cuts')
for tab in (gammas, background):
tab["selected_gh"] = evaluate_binned_cut(tab["gh_score"],
tab["reco_energy"], gh_cuts,
operator.ge)
gammas["selected_theta"] = evaluate_binned_cut(gammas["theta"],
gammas["reco_energy"],
theta_cuts, operator.le)
gammas["selected"] = gammas["selected_theta"] & gammas["selected_gh"]
# scale relative sensitivity by Crab flux to get the flux sensitivity
spectrum = particles['gamma']['target_spectrum']
sensitivity["flux_sensitivity"] = (
sensitivity["relative_sensitivity"] *
spectrum(sensitivity['reco_energy_center']))
log.info('Calculating IRFs')
hdus = [
fits.PrimaryHDU(),
fits.BinTableHDU(sensitivity, name="SENSITIVITY"),
fits.BinTableHDU(theta_cuts, name="THETA_CUTS"),
fits.BinTableHDU(gh_cuts, name="GH_CUTS"),
]
masks = {
"": gammas["selected"],
"_NO_CUTS": slice(None),
"_ONLY_GH": gammas["selected_gh"],
"_ONLY_THETA": gammas["selected_theta"],
}
# binnings for the irfs
true_energy_bins = add_overflow_bins(
create_bins_per_decade(10**-1.9 * u.TeV, 10**2.31 * u.TeV, 10))
reco_energy_bins = add_overflow_bins(
create_bins_per_decade(10**-1.9 * u.TeV, 10**2.31 * u.TeV, 5))
fov_offset_bins = [0, 0.5] * u.deg
source_offset_bins = np.arange(0, 1 + 1e-4, 1e-3) * u.deg
energy_migration_bins = np.geomspace(0.2, 5, 200)
for label, mask in masks.items():
effective_area = effective_area_per_energy(
gammas[mask],
particles["gamma"]["simulation_info"],
true_energy_bins=true_energy_bins,
)
hdus.append(
create_aeff2d_hdu(
effective_area[...,
np.newaxis], # add one dimension for FOV offset
true_energy_bins,
fov_offset_bins,
extname="EFFECTIVE_AREA" + label,
))
edisp = energy_dispersion(
gammas[mask],
true_energy_bins=true_energy_bins,
fov_offset_bins=fov_offset_bins,
migration_bins=energy_migration_bins,
)
hdus.append(
create_energy_dispersion_hdu(
edisp,
true_energy_bins=true_energy_bins,
migration_bins=energy_migration_bins,
fov_offset_bins=fov_offset_bins,
extname="ENERGY_DISPERSION" + label,
))
bias_resolution = energy_bias_resolution(gammas[gammas["selected"]],
reco_energy_bins,
energy_type="reco")
ang_res = angular_resolution(gammas[gammas["selected_gh"]],
reco_energy_bins,
energy_type="reco")
psf = psf_table(
gammas[gammas["selected_gh"]],
true_energy_bins,
fov_offset_bins=fov_offset_bins,
source_offset_bins=source_offset_bins,
)
background_rate = background_2d(
background[background['selected_gh']],
reco_energy_bins,
fov_offset_bins=np.arange(0, 11) * u.deg,
t_obs=T_OBS,
)
hdus.append(
create_background_2d_hdu(
background_rate,
reco_energy_bins,
fov_offset_bins=np.arange(0, 11) * u.deg,
))
hdus.append(
create_psf_table_hdu(
psf,
true_energy_bins,
source_offset_bins,
fov_offset_bins,
))
hdus.append(
create_rad_max_hdu(theta_cuts["cut"][:, np.newaxis], theta_bins,
fov_offset_bins))
hdus.append(fits.BinTableHDU(ang_res, name="ANGULAR_RESOLUTION"))
hdus.append(
fits.BinTableHDU(bias_resolution, name="ENERGY_BIAS_RESOLUTION"))
log.info('Writing outputfile')
fits.HDUList(hdus).writeto("pyirf_eventdisplay.fits.gz", overwrite=True)
ax.set_title("Residual")
ax.tick_labels.hide_y()
ax.axis_labels.hide_y()
plt.tight_layout(pad=4.0, w_pad=0.5)
plt.savefig(output_dir / f"continuum_model.{image_format}")
if do_plot:
plt.show()
else:
plt.clf()
plt.close()
# 5th step: 2D-Gauss fit on the cube map
print("#5: 2D-Gauss fit on the cube map")
alldata = table.QTable()
h = fc.gauss_fit(
cube_array,
mode="deg",
amplitude=f.peak,
x_mean=f.x_mean,
y_mean=f.y_mean,
x_stddev=f.x_stddev,
y_stddev=f.y_stddev,
theta=f.theta,
fixed={"x_mean": True, "y_mean": True, "theta": True},
)
for exch in exchs:
h.peak[exch] = np.nan
fig.tight_layout()
fig.savefig(output_dir / f"continuum_image.{image_format}")
if do_plot:
plt.show()
else:
plt.clf()
plt.close()
# 4th step: 2D-Gauss fit on the continuum map
print("#4: 2D-Gauss fit on the continuum map")
alldata = table.QTable(
names=(
"peak",
"x_mean",
"y_mean",
"x_stddev",
"y_stddev",
"theta",
)
)
amplitude = float(cont_array.max().values)
x_mean = float(cont_array.where(cont_array == cont_array.max(), drop=True).x.values)
y_mean = float(cont_array.where(cont_array == cont_array.max(), drop=True).y.values)
x_stddev = params["fitting"]["x_stddev"]
y_stddev = params["fitting"]["y_stddev"]
theta = params["fitting"]["theta"]
f = fc.gauss_fit(
cont_array,
mode="deg",
def into_vorbins(data_pix,
pix,
targetSN,
x="x",
y="y",
id="id",
n="N",
npix="Npix",
sn="SN",
signal=None,
noise=None,
quiet=False,
vquiet=True):
"""
Put pixels into Voronoi bins. This is a wrapper for voronoi.bin2d (see
https://github.com/lauralwatkins/voronoi) that does a lot of the tedious
housekeeping. There are two outputs:
1) an astropy QTable for the bins with the bin ID number, x-centre,
y-centre, number of objects, number of pixels, signal-to-noise, signal
and noise;
2) an array containing the bin ID number of all datapoints.
The code also adds to columns to the input pixel table (pix): "bin"
records the bin ID number of the pixels, and "Nbin" records the number of
stars in the bin to which the pixel belongs.
INPUTS
data_pix : pixel number of each datapoint
pix : pixel grid for the data
targetSN : target signal-to-noise required for binning
OPTIONS
x : name for x-coordinate column of input/output table [default "x"]
y : name for y-coordinate column of input/output table [default "y"]
id : name for bin ID column of output table [default "id"]
n : name for number of datapoints column of inout/output table
[default "N"]
npix : name for number of pixels column of output table [default "Npix"]
sn : name for signal-to-noise column of output table [default "SN"]
signal : name for signal column of input/output table [default None](*)
noise : name for noise column of input/output table [default None](**)
quiet : suppress text outputs for this code? [default False]
vquiet : suppress text outputs for Voronoi call? [default True]
(*) The code uses the number of objects in the pixel for the "signal" in
the pixel, unless a column name is passed for the signal data.
(**) The code also assumes that the noise in the pixel is the square-root
of the signal in the pixel (useful if the signal is the number of objects
in the pixel), unless a column name is passed for the noise data.
"""
import voronoi
# fail if there are no columns called n, x or y
for key in (n, x, y):
if key not in pix.colnames:
print("ERROR: Could not find column '{:}' in pixel table."\
.format(key))
return
# settings for Voronoi binning
good = pix[n] > 0
if not signal: signal = n
pix_signal = pix[good][signal]
if not noise: pix_noise = np.sqrt(pix[good][signal])
else: pix_noise = pix[good][noise]
# need to have pixels on same scale for Voronoi
xp = ((pix[x] - pix[x].min()) / pix.meta["xscale"])[good]
yp = ((pix[y] - pix[y].min()) / pix.meta["yscale"])[good]
# do the Voronoi binning
bin = table.QTable()
pix["bin"] = -np.ones(len(pix), dtype="int")
pix["bin"][good], bin[x], bin[y], bin[sn], bin[npix], vscale \
= voronoi.bin2d(xp, yp, pix_signal, pix_noise, targetSN, graphs=False,
quiet=vquiet)
bin["id"] = range(len(bin))
# adjust bins back to real scale
bin[x] = bin[x] * pix.meta["xscale"] + pix[x].min()
bin[y] = bin[y] * pix.meta["yscale"] + pix[y].min()
# bin number for each datapoint
data_bin = pix["bin"][data_pix]
# number of datapoints in each bin
bin[n] = np.array([sum(data_bin == i) for i in range(len(bin))])
# reorder columns
bin = bin[id, x, y, n, npix, sn]
# make columns to record the signal and noise in each bin
if signal == n: signal = "signal"
if not noise: noise = "noise"
bin[signal] = [sum(pix_signal[pix[good]["bin"] == b["id"]]) for b in bin]
bin[noise] = [np.sqrt(sum(pix_noise[pix[good]["bin"]==b["id"]]**2)) \
for b in bin]
# number of datapoints in bin to which pixel belongs
pix["Nbin"] = -np.ones(len(pix), dtype="int")
pix["Nbin"][good] = bin[pix[good]["bin"]][n]
# signal and noise in bin to which pixel belongs
pix[signal + "_bin"] = [np.nan] * len(pix)
pix[noise + "_bin"] = [np.nan] * len(pix)
pix[signal + "_bin"][good] = bin[pix[good]["bin"]][signal]
pix[noise + "_bin"][good] = bin[pix[good]["bin"]][noise]
if not quiet:
print("\nVoronoi binning of pixels\n")
print(" bins: {:}".format(len(bin)))
print(" min S/N per bin: {:}".format(bin[sn].min()))
print(" max S/N per bin: {:}".format(bin[sn].max()))
print(" avg S/N per bin: {:}".format(bin[sn].mean()))
return bin, data_bin