def thermal_spectrum(self, thermtable=None):
"""Calculate thermal spectrum using
:func:`ThermalObservationMode.to_spectrum`.
Parameters
----------
thermtable : str or `None`
Thermal component table filename.
If `None`, uses ``stsynphot.config.conf.thermtable``.
Returns
-------
sp : `synphot.spectrum.SourceSpectrum`
Thermal spectrum in PHOTLAM.
Raises
------
synphot.exceptions.SynphotError
Calculation failed.
"""
thom = ThermalObservationMode(
self._obsmode, graphtable=self.gtname, comptable=self.ctname,
thermtable=thermtable)
try:
sp = thom.to_spectrum()
except IndexError as e: # pragma: no cover
raise synexceptions.SynphotError(f'Broken graph table: {repr(e)}')
return sp
def _get_wave_intersection(self):
"""Find wavelengths in Angstrom where
``stsynphot.config.conf.waveset_array`` intersects with
``stsynphot.spectrum.Vega``.
.. note:: No one knows why Vega is the chosen one.
"""
def_wave = conf.waveset_array # Angstrom
minw = min(def_wave)
maxw = max(def_wave)
# Refine min and max wavelengths using thermal components
for component in self.components[1:]:
emissivity = component.emissivity
if emissivity is not None:
w = emissivity.waveset.value # Angstrom
minw = max(minw, w.min())
maxw = min(maxw, w.max())
w = self._merge_em_wave()
result = w[(w > minw) & (w < maxw)]
# Intersect with Vega
if Vega is None:
raise synexceptions.SynphotError('Missing Vega spectrum.')
w = Vega.waveset.value # Angstrom
return result[(result > w.min()) & (result < w.max())]
def get_filenames(self, compnames):
"""Get filenames of given component names.
For multiple matches, only the first match is kept.
Parameters
----------
compnames : list of str
List of component names to search. Case-sensitive.
Returns
-------
files : list of str
List of matched filenames.
Raises
------
synphot.exceptions.SynphotError
Unmatched component name.
"""
files = []
for compname in compnames:
if compname not in (None, '', conf.clear_filter):
index = np.where(self.compnames == compname)[0]
if len(index) < 1:
raise synexceptions.SynphotError(
'Cannot find {0} in {1}.'.format(compname, self.name))
files.append(self.filenames[index[0]].lstrip())
else:
files.append(conf.clear_filter)
return files
def thermback(self, area=None, thermtable=None):
"""Calculate thermal background count rate for
``self.obsmode``.
Calculation uses
:func:`~stsynphot.observationmode.ObservationMode.thermal_spectrum`
to extract thermal component source spectrum in
PHOTLAM per square arcsec. Then this spectrum is
integrated and multiplied by detector pixel scale
and telescope collecting area to produce a count rate
in count/s/pix. This unit is non-standard but used widely
by STScI Exposure Time Calculator.
.. note::
Similar to IRAF SYNPHOT THERMBACK.
Parameters
----------
area : float, `~astropy.units.quantity.Quantity`, or `None`
Area that flux covers.
If not a Quantity, assumed to be in :math:`cm^{2}`.
If `None`, use `area`.
thermtable : str or `None`
Thermal component table filename.
If `None`, uses ``stsynphot.config.conf.thermtable``.
Returns
-------
bg : `~astropy.units.quantity.Quantity`
Thermal background count rate.
Raises
------
synphot.exceptions.SynphotError
Calculation failed.
"""
if self.obsmode.pixscale is None:
raise synexceptions.SynphotError(
'Undefined pixel scale for {0}.'.format(self.obsmode))
if area is None:
area = self.area
area = units.validate_quantity(area, units.AREA)
sp = self.obsmode.thermal_spectrum(thermtable=thermtable)
bg = sp.integrate() * self.obsmode.pixscale ** 2 * area
return bg.value * (u.count / u.s / u.pix)
def __init__(self, modelclass, obsmode=None, **kwargs):
if obsmode is None:
raise synexceptions.SynphotError('Missing OBSMODE.')
super(ObservationSpectralElement, self).__init__(modelclass, **kwargs)
self._obsmode = obsmode
self.meta['expr'] = str(obsmode)
# Check for zero bounds, if applicable
try:
self.bounded_by_zero()
except synexceptions.SynphotError: # pragma: no cover
warnings.warn(
'Zero-bound check not done due to undefined waveset.',
AstropyUserWarning)
def _read_table(filename, ext, dtypes):
"""Generic table reader.
Parameters
----------
filename : str
Table filename.
If suffix is not 'fits' or 'fit', assume ASCII format.
ext : int
Data extension.
This is ignored for ASCII file.
dtypes : dict
Dictionary that maps column names to data types.
Returns
-------
data : `~astropy.io.fits.FITS_rec` or `~astropy.table.Table`
Data table.
Raises
------
synphot.exceptions.SynphotError
Failure to parse table.
"""
# FITS
if filename.endswith('.fits') or filename.endswith('.fit'):
with fits.open(filename) as f:
data = f[ext].data.copy()
err_str = ''
for key, val in dtypes.items():
if not np.issubdtype(data[key].dtype, val):
err_str += 'Expect {0} to be {1} but get {2}.\n'.format(
key, val, data[key].dtype)
if err_str:
raise synexceptions.SynphotError(err_str)
# ASCII
else: # pragma: no cover
converters = dict([[k, ascii.convert_numpy(v)]
for k, v in dtypes.items()])
data = ascii.read(filename, converters=converters)
return data
def from_obsmode(cls,
obsmode,
graphtable=None,
comptable=None,
component_dict={}):
"""Create a bandpass from observation mode string.
Parameters
----------
obsmode : str
Observation mode.
graphtable : str or `None`
Graph table filename.
If `None`, uses ``stsynphot.config.conf.graphtable``.
comptable : str or `None`
Optical component table filename.
If `None`, uses ``stsynphot.config.conf.comptable``.
component_dict : dict
Maps component filename to corresponding
`~stsynphot.observationmode.Component`.
Returns
-------
bp : `ObservationSpectralElement`
Empirical bandpass.
Raises
------
synphot.exceptions.SynphotError
Observation mode yields no throughput.
"""
from .observationmode import ObservationMode # Avoid circular import
ob = ObservationMode(obsmode,
graphtable=graphtable,
comptable=comptable,
component_dict=component_dict)
if not isinstance(ob.throughput, SpectralElement): # pragma: no cover
raise synexceptions.SynphotError(
'{0} has no throughput.'.format(obsmode))
return cls(ob.throughput, obsmode=ob)
def get_catalog_index(gridname):
"""Extract catalog index (grid parameters).
It is read once and then cached until the cache is cleared explicitly using
:func:`reset_cache`.
Parameters
----------
gridname : str
See :func:`grid_to_spec`.
Returns
-------
cat_index : list
List of ``[t_eff, metallicity, log_g, filename]``.
catdir : str
Directory containing the requested catalog.
"""
if gridname == 'ck04models':
catdir = 'crgridck04$'
elif gridname == 'k93models':
catdir = 'crgridk93$'
elif gridname == 'phoenix':
catdir = 'crgridphoenix$'
else:
raise synexceptions.SynphotError(
f'{gridname} is not a supported catalog grid.')
catdir = stio.irafconvert(catdir)
filename = stio.resolve_filename(catdir, 'catalog.fits')
# If not cached, read from grid catalog and cache it
if filename not in _CACHE:
data = stio.read_catalog(filename) # EXT 1
_CACHE[filename] = [list(map(float, index.split(','))) +
[data['FILENAME'][i]]
for i, index in enumerate(data['INDEX'])]
return _CACHE[filename], catdir
def read_graphtable(filename, tab_ext=1):
"""Read graph table file.
Table must contain the following named columns:
#. ``COMPNAME`` - Component name, usually filter name (str)
#. ``KEYWORD`` - Usually instrument name (str)
#. ``INNODE`` - Input node number (int)
#. ``OUTNODE``- Output node number (int)
#. ``THCOMPNAME`` - Thermal component name, usually filter name (str)
#. ``COMMENT`` - Comment (str)
Example:
+--------+-------+------+-------+----------+--------+
|COMPNAME|KEYWORD|INNODE|OUTNODE|THCOMPNAME|COMMENT |
+========+=======+======+=======+==========+========+
| clear |nicmos | 1 | 30 | clear |idno=100|
+--------+-------+------+-------+----------+--------+
| clear | wfc3 | 1 | 30 | clear | |
+--------+-------+------+-------+----------+--------+
| clear | wfpc | 1 | 20 | clear |idno=100|
+--------+-------+------+-------+----------+--------+
Parameters
----------
filename : str
Graph table filename.
If suffix is not 'fits' or 'fit', assume ASCII format.
tab_ext : int, optional
FITS extension index of the data table.
This is ignored for ASCII file.
Returns
-------
primary_area : `~astropy.units.quantity.Quantity` or `None`
Value of PRIMAREA keyword in primary header.
Always `None` for ASCII file.
data : `~astropy.io.fits.FITS_rec` or `~astropy.table.Table`
Data table.
Raises
------
synphot.exceptions.SynphotError
Failure to parse graph table.
"""
graph_dtypes = {
'COMPNAME': np.str_,
'KEYWORD': np.str_,
'INNODE': np.int32,
'OUTNODE': np.int32,
'THCOMPNAME': np.str_,
'COMMENT': np.str_
}
data = _read_table(filename, tab_ext, graph_dtypes)
# Get primary area
if filename.endswith('.fits') or filename.endswith('.fit'):
with fits.open(filename) as f:
primary_area = f[str('PRIMARY')].header.get('PRIMAREA', None)
else: # pragma: no cover
primary_area = None
if primary_area is not None and not isinstance(primary_area, u.Quantity):
primary_area = primary_area * units.AREA
# Check for segmented graph table
if np.any([x.lower().endswith('graph')
for x in data['COMPNAME']]): # pragma: no cover
raise synexceptions.SynphotError(
'Segmented graph tables not supported.')
return primary_area, data
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 grid_to_spec(gridname, t_eff, metallicity, log_g):
"""Extract spectrum from given catalog grid parameters.
Interpolate if necessary.
Grid parameters are only read once and then cached.
Until the cache is cleared explicitly using
:func:`reset_cache`, cached values are used.
Parameters
----------
gridname : {'ck04models', 'k93models', 'phoenix'}
Model to use:
* ``ck04models`` - Castelli & Kurucz (2004)
* ``k93models`` - Kurucz (1993)
* ``phoenix`` - Allard et al. (2009)
t_eff : str, float or `astropy.units.quantity.Quantity`
Effective temperature of model.
If not Quantity, assumed to be in Kelvin.
If string (from parser), convert to Quantity.
metallicity : str or float
Metallicity of model.
If string (from parser), convert to float.
log_g : str or float
Log surface gravity for model.
If string (from parser), convert to float.
Returns
-------
sp : `synphot.spectrum.SourceSpectrum`
Empirical source spectrum.
Raises
------
stsynphot.exceptions.ParameterOutOfBounds
Grid parameter out of bounds.
synphot.exceptions.SynphotError
Invalid inputs.
"""
if gridname == 'ck04models':
catdir = 'crgridck04$'
elif gridname == 'k93models':
catdir = 'crgridk93$'
elif gridname == 'phoenix':
catdir = 'crgridphoenix$'
else:
raise synexceptions.SynphotError(
'{0} is not a supported catalog grid.'.format(gridname))
metallicity = _par_from_parser(metallicity)
if isinstance(metallicity, u.Quantity):
raise synexceptions.SynphotError(
'Quantity is not supported for metallicity.')
log_g = _par_from_parser(log_g)
if isinstance(log_g, u.Quantity):
raise synexceptions.SynphotError(
'Quantity is not supported for log surface gravity.')
t_eff = units.validate_quantity(_par_from_parser(t_eff), u.K).value
catdir = stio.irafconvert(catdir)
filename = os.path.join(catdir, 'catalog.fits')
# If not cached, read from grid catalog and cache it
if filename not in _CACHE:
data = stio.read_catalog(filename) # Ext 1
_CACHE[filename] = [[float(x) for x in index.split(',')] +
[data['FILENAME'][i]]
for i, index in enumerate(data['INDEX'])]
indices = _CACHE[filename]
list0, list1 = _break_list(indices, 0, t_eff)
list2, list3 = _break_list(list0, 1, metallicity)
list4, list5 = _break_list(list1, 1, metallicity)
list6, list7 = _break_list(list2, 2, log_g)
list8, list9 = _break_list(list3, 2, log_g)
list10, list11 = _break_list(list4, 2, log_g)
list12, list13 = _break_list(list5, 2, log_g)
sp1 = _get_spectrum(list6[0], catdir)
sp2 = _get_spectrum(list7[0], catdir)
sp3 = _get_spectrum(list8[0], catdir)
sp4 = _get_spectrum(list9[0], catdir)
sp5 = _get_spectrum(list10[0], catdir)
sp6 = _get_spectrum(list11[0], catdir)
sp7 = _get_spectrum(list12[0], catdir)
sp8 = _get_spectrum(list13[0], catdir)
spa1 = _interpolate_spectrum(sp1, sp2, log_g)
spa2 = _interpolate_spectrum(sp3, sp4, log_g)
spa3 = _interpolate_spectrum(sp5, sp6, log_g)
spa4 = _interpolate_spectrum(sp7, sp8, log_g)
spa5 = _interpolate_spectrum(spa1, spa2, metallicity)
spa6 = _interpolate_spectrum(spa3, spa4, metallicity)
spa7 = _interpolate_spectrum(spa5, spa6, t_eff)
sp = spa7[0]
sp.meta['expr'] = '{0}(T_eff={1:g},metallicity={2:g},log_g={3:g})'.format(
gridname, t_eff, metallicity, log_g)
return sp
def grid_to_spec(gridname, t_eff, metallicity, log_g):
"""Extract spectrum from given catalog grid parameters.
Interpolate if necessary.
Grid parameters are read with :func:`get_catalog_index`.
Parameters
----------
gridname : {'ck04models', 'k93models', 'phoenix'}
Model to use:
* ``ck04models`` - Castelli & Kurucz (2004)
* ``k93models`` - Kurucz (1993)
* ``phoenix`` - Allard et al. (2009)
t_eff : str, float or `astropy.units.quantity.Quantity`
Effective temperature of model.
If not Quantity, assumed to be in Kelvin.
If string (from parser), convert to Quantity.
metallicity : str or float
Metallicity of model.
If string (from parser), convert to float.
log_g : str or float
Log surface gravity for model.
If string (from parser), convert to float.
Returns
-------
sp : `synphot.spectrum.SourceSpectrum`
Empirical source spectrum.
Raises
------
stsynphot.exceptions.ParameterOutOfBounds
Grid parameter out of bounds.
synphot.exceptions.SynphotError
Invalid inputs.
"""
indices, catdir = get_catalog_index(gridname)
metallicity = _par_from_parser(metallicity)
if isinstance(metallicity, u.Quantity):
raise synexceptions.SynphotError(
'Quantity is not supported for metallicity.')
log_g = _par_from_parser(log_g)
if isinstance(log_g, u.Quantity):
raise synexceptions.SynphotError(
'Quantity is not supported for log surface gravity.')
t_eff = units.validate_quantity(_par_from_parser(t_eff), u.K).value
list0, list1 = _break_list(indices, 0, t_eff)
list2, list3 = _break_list(list0, 1, metallicity)
list4, list5 = _break_list(list1, 1, metallicity)
list6, list7 = _break_list(list2, 2, log_g)
list8, list9 = _break_list(list3, 2, log_g)
list10, list11 = _break_list(list4, 2, log_g)
list12, list13 = _break_list(list5, 2, log_g)
sp1 = _get_spectrum(list6[0], catdir)
sp2 = _get_spectrum(list7[0], catdir)
sp3 = _get_spectrum(list8[0], catdir)
sp4 = _get_spectrum(list9[0], catdir)
sp5 = _get_spectrum(list10[0], catdir)
sp6 = _get_spectrum(list11[0], catdir)
sp7 = _get_spectrum(list12[0], catdir)
sp8 = _get_spectrum(list13[0], catdir)
spa1 = _interpolate_spectrum(sp1, sp2, log_g)
spa2 = _interpolate_spectrum(sp3, sp4, log_g)
spa3 = _interpolate_spectrum(sp5, sp6, log_g)
spa4 = _interpolate_spectrum(sp7, sp8, log_g)
spa5 = _interpolate_spectrum(spa1, spa2, metallicity)
spa6 = _interpolate_spectrum(spa3, spa4, metallicity)
spa7 = _interpolate_spectrum(spa5, spa6, t_eff)
sp = spa7[0]
sp.meta['expr'] = (f'{gridname}(T_eff={t_eff:g},'
f'metallicity={metallicity:g},log_g={log_g:g})')
return sp
