def _loader(self):
"""
Load a template from the database
Returns
-------
meta: metadata of the spectra (header)
lam: wavelengths
flux: flux
"""
try:
self.wave_unit = units.validate_unit(self.wave_unit)
self.flux_unit = units.validate_unit(self.flux_unit)
except exceptions.SynphotError: # Assumes angtroms and FLAM
self.wave_unit = u.AA
self.flux_unit = units.FLAM
# self.resolution = self.resolution * self.wave_unit
if self.data_type == "fits": # make try and except here to catch most problems
meta, lam, flux = read_fits_spec(self.path,
ext=1,
wave_unit=self.wave_unit,
flux_unit=self.flux_unit,
wave_col=self.wave_column_name,
flux_col=self.flux_column_name)
else:
meta, lam, flux = read_ascii_spec(self.path,
wave_unit=self.wave_unit,
flux_unit=self.flux_unit)
return meta, lam, flux
def _loader(self):
"""
Load a filter from the database
Returns
-------
meta: metadata of the spectra (header)
lam: wavelengths
flux: flux
"""
try: # it should also try to read it from the file directly
self.wave_unit = units.validate_unit(self.wave_unit)
except exceptions.SynphotError:
self.wave_unit = u.AA
# make try and except here to catch most problems
if self.data_type == "fits":
meta, lam, trans = read_fits_spec(self.filename,
ext=1,
wave_unit=self.wave_unit)
# wave_col=self.wave_column_name, flux_col=self.trans_column_name)
elif self.data_type == "ascii":
meta, lam, trans = read_ascii_spec(self.filename,
wave_unit=self.wave_unit)
# wave_col=self.wave_column_name, flux_col=self.trans_column_name)
# , flux_unit=self._internal_flux_unit,
lam = lam.to(u.AA)
return meta, lam, trans.value
def _loader(self):
"""
Load a filter from the database
Returns
-------
meta: metadata of the spectra (header)
lam: wavelengths
flux: flux
"""
try: # it should also try to read it from the file directly
self.wave_unit = units.validate_unit(self.wave_unit)
except exceptions.SynphotError:
self.wave_unit = u.AA
if self.data_type == "fits":
meta, lam, rvs = read_fits_spec(
self.filename,
ext=1,
wave_unit=self.wave_unit,
flux_unit=self.extinction_unit,
# self._internal_flux_unit,
wave_col=self.wave_column,
flux_col=self.extinction_column)
elif self.data_type == "ascii":
meta, lam, rvs = read_ascii_spec(
self.filename,
wave_unit=self.wave_unit,
flux_unit=self.extinction_unit,
# self._internal_flux_unit,
wave_col=self.wave_column,
flux_col=self.extinction_column)
return meta, lam, rvs
def interpolate_spectral_element(parfilename, interpval, ext=1):
"""Interpolate (or extrapolate) throughput spectra in given
parameterized FITS table to given parameter value.
FITS table is parsed with :func:`stsynphot.stio.read_interp_spec`.
Parameterized values must be in ascending order in the
table columns.
If extrapolation is needed but not allowed, default throughput
from ``THROUGHPUT`` column will be used.
Parameters
----------
parfilename : str
Parameterized filename contains a suffix followed by
a column name specificationin between square brackets.
For example, ``path/acs_fr656n_006_syn.fits[fr656n#]``.
interpval : float
Desired parameter value.
ext : int, optional
FITS extension index of the data table.
Returns
-------
sp : `synphot.spectrum.SpectralElement`
Empirical bandpass at ``interpval``.
Raises
------
synphot.exceptions.ExtrapolationNotAllowed
Extrapolation is not allowed by data table.
synphot.exceptions.SynphotError
No columns available for interpolation or extrapolation.
"""
def_colname = 'THROUGHPUT'
warndict = {}
# Separate real filename and column name specification
xre = _interpfilepatt.search(parfilename)
if xre is None:
raise synexceptions.SynphotError(
'{0} must be in the format of "path/filename.fits'
'[col#]"'.format(parfilename))
filename = parfilename[0:xre.start()]
col_prefix = xre.group('col').upper()
# Read data table
data, wave_unit, doshift, extrapolate = stio.read_interp_spec(
filename, tab_ext=ext)
wave_unit = units.validate_unit(wave_unit)
wave0 = data['WAVELENGTH']
# Determine the columns that bracket the desired value.
# Grab all columns that begin with the parameter name (e.g. 'MJD#')
# and then split off the numbers after the '#'.
col_names = []
col_pars = []
for n in data.names:
cn = n.upper()
if cn.startswith(col_prefix):
col_names.append(cn)
col_pars.append(float(cn.split('#')[1]))
if len(col_names) < 1:
raise synexceptions.SynphotError(
'{0} contains no interpolated columns for {1}.'.format(
filename, col_prefix))
# Assumes ascending order of parameter values in table.
min_par = col_pars[0]
max_par = col_pars[-1]
# Exact match. No interpolation needed.
if interpval in col_pars:
thru = data[col_names[col_pars.index(interpval)]]
# Need interpolation.
elif (interpval > min_par) and (interpval < max_par):
upper_ind = np.searchsorted(col_pars, interpval)
lower_ind = upper_ind - 1
thru = _interp_spec(
interpval, wave0, col_pars[lower_ind], col_pars[upper_ind],
data[col_names[lower_ind]], data[col_names[upper_ind]], doshift)
# Need extrapolation, if allowed.
elif extrapolate:
# Extrapolate below lowest columns.
if interpval < min_par:
thru = _extrap_spec(interpval, min_par, col_pars[1],
data[col_names[0]], data[col_names[1]])
# Extrapolate above highest columns.
else: # interpval > max_par
thru = _extrap_spec(interpval, col_pars[-2], max_par,
data[col_names[-2]], data[col_names[-1]])
# Extrapolation not allowed.
else:
# Use default, if available.
if def_colname in data.names:
warnings.warn(
'Extrapolation not allowed, using default throughput for '
'{0}.'.format(parfilename), AstropyUserWarning)
warndict['DefaultThroughput'] = True
thru = data[def_colname]
# Nothing can be done.
else:
raise synexceptions.ExtrapolationNotAllowed(
'No default throughput for {0}.'.format(parfilename))
meta = {'expr': '{0}#{1:g}'.format(filename, interpval),
'warnings': warndict}
return SpectralElement(
Empirical1D, points=wave0*wave_unit, lookup_table=thru, meta=meta)
def p_functioncall(self, tree):
# Where all the real interpreter action is.
# Note that things that should only be done at the top level
# are performed in :func:`interpret` defined below.
""" V ::= function_call ( V LPAREN V RPAREN ) """
if not isinstance(tree[2].value, list):
args = [tree[2].value]
else:
args = tree[2].value
fname = tree[0].value
metadata = {'expr': '{0}{1}'.format(fname, tuple(args))}
if fname not in _SYFUNCTIONS:
log.error('Unknown function: {0}'.format(fname))
self.error(fname)
else:
# Constant spectrum
if fname == 'unit':
if args[1] not in _SYFORMS:
log.error('Unrecognized unit: {0}'.format(args[1]))
self.error(fname)
try:
fluxunit = units.validate_unit(args[1])
tree.value = SourceSpectrum(ConstFlux1D,
amplitude=args[0] * fluxunit,
meta=metadata)
except NotImplementedError as e:
log.error(str(e))
self.error(fname)
# Black body
elif fname == 'bb':
tree.value = SourceSpectrum(BlackBodyNorm1D,
temperature=args[0])
# Power law
elif fname == 'pl':
if args[2] not in _SYFORMS:
log.error('Unrecognized unit: {0}'.format(args[2]))
self.error(fname)
try:
fluxunit = units.validate_unit(args[2])
tree.value = SourceSpectrum(PowerLawFlux1D,
amplitude=1 * fluxunit,
x_0=args[0],
alpha=-args[1],
meta=metadata)
except (synexceptions.SynphotError, NotImplementedError) as e:
log.error(str(e))
self.error(fname)
# Box throughput
elif fname == 'box':
tree.value = SpectralElement(Box1D,
amplitude=1,
x_0=args[0],
width=args[1],
meta=metadata)
# Source spectrum from file
elif fname == 'spec':
tree.value = SourceSpectrum.from_file(irafconvert(args[0]))
tree.value.meta.update(metadata)
# Passband
elif fname == 'band':
tree.value = spectrum.band(tree[2].svalue)
tree.value.meta.update(metadata)
# Gaussian emission line
elif fname == 'em':
if args[3] not in _SYFORMS:
log.error('Unrecognized unit: {0}'.format(args[3]))
self.error(fname)
x0 = args[0]
fluxunit = units.validate_unit(args[3])
totflux = units.convert_flux(x0, args[2] * fluxunit,
units.PHOTLAM).value
tree.value = SourceSpectrum(GaussianFlux1D,
total_flux=totflux,
mean=x0,
fwhm=args[1])
# Catalog interpolation
elif fname == 'icat':
tree.value = grid_to_spec(*args)
# Renormalize source spectrum
elif fname == 'rn':
sp = args[0]
bp = args[1]
fluxunit = units.validate_unit(args[3])
rnval = args[2] * fluxunit
if not isinstance(sp, SourceSpectrum):
sp = SourceSpectrum.from_file(irafconvert(sp))
if not isinstance(bp, SpectralElement):
bp = SpectralElement.from_file(irafconvert(bp))
# Always force the renormalization to occur: prevent exceptions
# in case of partial overlap. Less robust but duplicates
# IRAF SYNPHOT. Force the renormalization in the case of
# partial overlap, but raise an exception if the spectrum and
# bandpass are entirely disjoint.
try:
tree.value = sp.normalize(rnval,
band=bp,
area=conf.area,
vegaspec=spectrum.Vega)
except synexceptions.PartialOverlap:
tree.value = sp.normalize(rnval,
band=bp,
area=conf.area,
vegaspec=spectrum.Vega,
force=True)
tree.value.warnings = {
'force_renorm': ('Renormalization exceeds the limit '
'of the specified passband.')
}
tree.value.meta.update(metadata)
# Redshift source spectrum (flat spectrum if fails)
elif fname == 'z':
sp = args[0]
# ETC generates junk (i.e., 'null') sometimes
if isinstance(sp, str) and sp != 'null':
sp = SourceSpectrum.from_file(irafconvert(sp))
if isinstance(sp, SourceSpectrum):
tree.value = sp
tree.value.z = args[1]
else:
tree.value = SourceSpectrum(ConstFlux1D, amplitude=1)
tree.value.meta.update(metadata)
# Extinction
elif fname == 'ebmvx':
try:
tree.value = spectrum.ebmvx(args[1], args[0])
except synexceptions.SynphotError as e:
log.error(str(e))
self.error(fname)
tree.value.meta.update(metadata)
# Default
else:
tree.value = ('would call {0} with the following args: '
'{1}'.format(fname, repr(args)))
def interpolate_spectral_element(parfilename, interpval, ext=1):
"""Interpolate (or extrapolate) throughput spectra in given
parameterized FITS table to given parameter value.
FITS table is parsed with :func:`stsynphot.stio.read_interp_spec`.
Parameterized values must be in ascending order in the
table columns.
If extrapolation is needed but not allowed, default throughput
from ``THROUGHPUT`` column will be used.
Parameters
----------
parfilename : str
Parameterized filename contains a suffix followed by
a column name specificationin between square brackets.
For example, ``path/acs_fr656n_006_syn.fits[fr656n#]``.
interpval : float
Desired parameter value.
ext : int, optional
FITS extension index of the data table.
Returns
-------
sp : `synphot.spectrum.SpectralElement`
Empirical bandpass at ``interpval``.
Raises
------
synphot.exceptions.ExtrapolationNotAllowed
Extrapolation is not allowed by data table.
synphot.exceptions.SynphotError
No columns available for interpolation or extrapolation.
"""
def_colname = 'THROUGHPUT'
warndict = {}
# Separate real filename and column name specification
xre = _interpfilepatt.search(parfilename)
if xre is None:
raise synexceptions.SynphotError(
'{0} must be in the format of "path/filename.fits'
'[col#]"'.format(parfilename))
filename = parfilename[0:xre.start()]
col_prefix = xre.group('col').upper()
# Read data table
data, wave_unit, doshift, extrapolate = stio.read_interp_spec(
filename, tab_ext=ext)
wave_unit = units.validate_unit(wave_unit)
wave0 = data['WAVELENGTH']
# Determine the columns that bracket the desired value.
# Grab all columns that begin with the parameter name (e.g. 'MJD#')
# and then split off the numbers after the '#'.
col_names = []
col_pars = []
for n in data.names:
cn = n.upper()
if cn.startswith(col_prefix):
col_names.append(cn)
col_pars.append(float(cn.split('#')[1]))
if len(col_names) < 1:
raise synexceptions.SynphotError(
'{0} contains no interpolated columns for {1}.'.format(
filename, col_prefix))
# Assumes ascending order of parameter values in table.
min_par = col_pars[0]
max_par = col_pars[-1]
# Exact match. No interpolation needed.
if interpval in col_pars:
thru = data[col_names[col_pars.index(interpval)]]
# Need interpolation.
elif (interpval > min_par) and (interpval < max_par):
upper_ind = np.searchsorted(col_pars, interpval)
lower_ind = upper_ind - 1
thru = _interp_spec(
interpval, wave0, col_pars[lower_ind], col_pars[upper_ind],
data[col_names[lower_ind]], data[col_names[upper_ind]], doshift)
# Need extrapolation, if allowed.
elif extrapolate:
# Extrapolate below lowest columns.
if interpval < min_par:
thru = _extrap_spec(interpval, min_par, col_pars[1],
data[col_names[0]], data[col_names[1]])
# Extrapolate above highest columns.
else: # interpval > max_par
thru = _extrap_spec(interpval, col_pars[-2], max_par,
data[col_names[-2]], data[col_names[-1]])
# Extrapolation not allowed.
else:
# Use default, if available.
if def_colname in data.names:
warnings.warn(
'Extrapolation not allowed, using default throughput for '
'{0}.'.format(parfilename), AstropyUserWarning)
warndict['DefaultThroughput'] = True
thru = data[def_colname]
# Nothing can be done.
else:
raise synexceptions.ExtrapolationNotAllowed(
'No default throughput for {0}.'.format(parfilename))
meta = {'expr': '{0}#{1:g}'.format(filename, interpval),
'warnings': warndict}
return SpectralElement(
Empirical1D, points=wave0 * wave_unit, lookup_table=thru, meta=meta)