def set_units(self, disp_unit, data_unit):
if self.dispersion_unit.is_equivalent(disp_unit,
equivalencies=spectral()):
self._dispersion = self.dispersion.data.to(
disp_unit, equivalencies=spectral()).value
# Finally, change the unit
self.dispersion_unit = disp_unit
else:
logging.warning("Units are not compatible.")
if self.unit.is_equivalent(data_unit,
equivalencies=spectral_density(
self.dispersion.data)):
self._data = self.data.data.to(
data_unit, equivalencies=spectral_density(
self.dispersion.data)).value
self._uncertainty = self._uncertainty.__class__(
self.raw_uncertainty.data.to(
data_unit, equivalencies=spectral_density(
self.dispersion.data)).value)
# Finally, change the unit
self._unit = data_unit
else:
logging.warning("Units are not compatible.")
def bandflux(self, band):
"""Perform synthentic photometry in a given bandpass.
The bandpass transmission is interpolated onto the wavelength grid
of the spectrum. The result is a weighted sum of the spectral flux
density values (weighted by transmission values).
Parameters
----------
band : Bandpass object or name of registered bandpass.
Returns
-------
bandflux : float
Total flux in ph/s/cm^2. If part of bandpass falls
outside the spectrum, `None` is returned instead.
bandfluxerr : float
Error on flux. Only returned if the `error` attribute is not
`None`.
"""
band = get_bandpass(band)
bwave, btrans = band.to_unit(self._wunit)
if (bwave[0] < self._wave[0] or
bwave[-1] > self._wave[-1]):
return None
idx = ((self._wave > bwave[0]) &
(self._wave < bwave[-1]))
d = self._wave[idx]
f = self._flux[idx]
#TODO: use spectral density equivalencies once they can do photons.
# first convert to ergs / s /cm^2 / (wavelength unit)
target_unit = u.erg / u.s / u.cm**2 / self._wunit
if self._unit != target_unit:
f = self._unit.to(target_unit, f,
u.spectral_density(self._wunit, d))
# Then convert ergs to photons: photons = Energy / (h * nu)
f = f / const.h.cgs.value / self._wunit.to(u.Hz, d, u.spectral())
trans = np.interp(d, bwave, btrans)
binw = np.gradient(d)
ftot = np.sum(f * trans * binw)
if self._error is None:
return ftot
else:
e = self._error[idx]
# Do the same conversion as above
if self._unit != target_unit:
e = self._unit.to(target_unit, e,
u.spectral_density(self._wunit, d))
e = e / const.h.cgs.value / self._wunit.to(u.Hz, d, u.spectral())
etot = np.sqrt(np.sum((e * binw) ** 2 * trans))
return ftot, etot
def from_config(cls, config, **kwargs):
"""
Create a new Simulation instance from a Configuration object.
Parameters
----------
config : tardis.io.config_reader.Configuration
**kwargs
Allow overriding some structures, such as model, plasma, atomic data
and the runner, instead of creating them from the configuration
object.
Returns
-------
Simulation
"""
# Allow overriding some config structures. This is useful in some
# unit tests, and could be extended in all the from_config classmethods.
if 'model' in kwargs:
model = kwargs['model']
else:
model = Radial1DModel.from_config(config)
if 'plasma' in kwargs:
plasma = kwargs['plasma']
else:
plasma = assemble_plasma(config, model,
atom_data=kwargs.get('atom_data', None))
if 'runner' in kwargs:
runner = kwargs['runner']
else:
runner = MontecarloRunner.from_config(config)
luminosity_nu_start = config.supernova.luminosity_wavelength_end.to(
u.Hz, u.spectral())
try:
luminosity_nu_end = config.supernova.luminosity_wavelength_start.to(
u.Hz, u.spectral())
except ZeroDivisionError:
luminosity_nu_end = np.inf * u.Hz
last_no_of_packets = config.montecarlo.last_no_of_packets
if last_no_of_packets is None or last_no_of_packets < 0:
last_no_of_packets = config.montecarlo.no_of_packets
last_no_of_packets = int(last_no_of_packets)
return cls(iterations=config.montecarlo.iterations,
model=model,
plasma=plasma,
runner=runner,
no_of_packets=int(config.montecarlo.no_of_packets),
no_of_virtual_packets=int(
config.montecarlo.no_of_virtual_packets),
luminosity_nu_start=luminosity_nu_start,
luminosity_nu_end=luminosity_nu_end,
last_no_of_packets=last_no_of_packets,
luminosity_requested=config.supernova.luminosity_requested.cgs,
convergence_strategy=config.montecarlo.convergence_strategy,
nthreads=config.montecarlo.nthreads)
def evaluate(self, packet_nu, packet_energy, virtual_nu, virtual_energy,
param_names, param_values):
packet_lambda = packet_nu.to(u.angstrom, u.spectral())
bin_counts = np.histogram(packet_lambda, bins=self.wavelength_bins)[0]
uncertainty = (np.sqrt(bin_counts) * np.mean(packet_energy)
/ np.diff(self.wavelength_bins))
if self.mode == 'normal':
luminosity = np.histogram(packet_lambda,
weights=packet_energy,
bins=self.wavelength_bins)[0]
elif self.mode == 'virtual':
virtual_packet_lambda = virtual_nu.to(u.angstrom, u.spectral())
luminosity = np.histogram(virtual_packet_lambda,
weights=virtual_energy,
bins=self.wavelength_bins)[0]
uncertainty /= self.virtual_uncertainty_scaling
luminosity_density = luminosity / np.diff(self.wavelength_bins)
self.luminosity_density = luminosity_density
self.uncertainty = uncertainty.value
return (self.observed_wavelength, luminosity_density, uncertainty.value,
param_names, param_values)
def test_equivalency_context_manager():
base_registry = u.get_current_unit_registry()
def just_to_from_units(equivalencies):
return [(equiv[0], equiv[1]) for equiv in equivalencies]
tf_dimensionless_angles = just_to_from_units(u.dimensionless_angles())
tf_spectral = just_to_from_units(u.spectral())
assert base_registry.equivalencies == []
with u.set_enabled_equivalencies(u.dimensionless_angles()):
new_registry = u.get_current_unit_registry()
assert (set(just_to_from_units(new_registry.equivalencies)) ==
set(tf_dimensionless_angles))
assert set(new_registry.all_units) == set(base_registry.all_units)
with u.set_enabled_equivalencies(u.spectral()):
newer_registry = u.get_current_unit_registry()
assert (set(just_to_from_units(newer_registry.equivalencies)) ==
set(tf_spectral))
assert (set(newer_registry.all_units) ==
set(base_registry.all_units))
assert (set(just_to_from_units(new_registry.equivalencies)) ==
set(tf_dimensionless_angles))
assert set(new_registry.all_units) == set(base_registry.all_units)
with u.add_enabled_equivalencies(u.spectral()):
newer_registry = u.get_current_unit_registry()
assert (set(just_to_from_units(newer_registry.equivalencies)) ==
set(tf_dimensionless_angles) | set(tf_spectral))
assert (set(newer_registry.all_units) ==
set(base_registry.all_units))
assert base_registry is u.get_current_unit_registry()
def test_convert_back(self, unit_from, unit_to,convention,ref_unit):
if unit_from in ('cms','cm/s','centimeter/second') or unit_to in ('cms','cm/s','centimeter/second'):
xvals = np.linspace(1000,10000,3)
else:
xvals = np.linspace(1,10,3)
assert not np.any(xvals==0.0)
# all conversions include a * or / by speedoflight_ms
threshold = np.spacing(units.speedoflight_ms) * 100
if 'megameter' in unit_from or 'Mm' in unit_from:
threshold *= 10
if 'centimeter' in unit_from or 'cm' in unit_from:
threshold *= 10
unit_to = u.Unit(unit_to)
unit_from = u.Unit(unit_from)
# come up with a sane reference value
if unit_from.physical_type in ('frequency','length'):
refX = u.Quantity(5, unit_from).to(ref_unit, u.spectral())
elif unit_to.physical_type in ('frequency','length'):
refX = u.Quantity(5, unit_to).to(ref_unit, u.spectral())
else:
refX = u.Quantity(5, ref_unit)
xarr = units.SpectroscopicAxis(np.copy(xvals), unit=unit_from, refX=refX,
velocity_convention=convention)
xarr.convert_to_unit(unit_to, velocity_convention=convention,
make_dxarr=False)
xarr.convert_to_unit(unit_from, velocity_convention=convention,
make_dxarr=False)
infinites = np.isinf(xarr.value)
assert all(np.abs((xarr.value - xvals)/xvals)[~infinites] < threshold)
assert xarr.unit == unit_from
def pixel_range(self, waverange, **kwargs):
"""Calculate the number of pixels within the given wavelength
range and ``self.binwave``.
Parameters
----------
waverange : tuple of float or `astropy.units.quantity.Quantity`
Lower and upper limits of the desired wavelength range.
If not a Quantity, assumed to be in the same unit as
``self.binwave``.
kwargs : dict
Keywords accepted by :func:`synphot.binning.pixel_range`.
Returns
-------
npix : number
Number of pixels.
Raises
------
synphot.exceptions.UndefinedBinset
Missing binned data.
"""
self._set_data(True) # Use binned data
w1 = units.validate_quantity(
waverange[0], self._wave.unit, equivalencies=u.spectral())
w2 = units.validate_quantity(
waverange[-1], self._wave.unit, equivalencies=u.spectral())
return binning.pixel_range(
self._wave.value, (w1.value, w2.value), **kwargs)
def test_equivalent_units2():
units = set(u.Hz.find_equivalent_units(u.spectral()))
match = set(
[u.AU, u.Angstrom, u.Hz, u.J, u.Ry, u.cm, u.eV, u.erg, u.lyr,
u.m, u.micron, u.pc, u.solRad, u.Bq, u.Ci, u.k, u.earthRad,
u.jupiterRad])
assert units == match
from astropy.units import imperial
with u.add_enabled_units(imperial):
units = set(u.Hz.find_equivalent_units(u.spectral()))
match = set(
[u.AU, u.Angstrom, imperial.BTU, u.Hz, u.J, u.Ry,
imperial.cal, u.cm, u.eV, u.erg, imperial.ft, imperial.fur,
imperial.inch, imperial.kcal, u.lyr, u.m, imperial.mi,
imperial.mil, u.micron, u.pc, u.solRad, imperial.yd, u.Bq, u.Ci,
imperial.nmi, u.k, u.earthRad, u.jupiterRad])
assert units == match
units = set(u.Hz.find_equivalent_units(u.spectral()))
match = set(
[u.AU, u.Angstrom, u.Hz, u.J, u.Ry, u.cm, u.eV, u.erg, u.lyr,
u.m, u.micron, u.pc, u.solRad, u.Bq, u.Ci, u.k, u.earthRad,
u.jupiterRad])
assert units == match
def parse_spectrum_list2dict(spectrum_list):
"""
Parse the spectrum list [start, stop, num] to a list
"""
if 'start' in spectrum_list and 'stop' in spectrum_list \
and 'num' in spectrum_list:
spectrum_list = [spectrum_list['start'], spectrum_list['stop'],
spectrum_list['num']]
if spectrum_list[0].unit.physical_type != 'length' and \
spectrum_list[1].unit.physical_type != 'length':
raise ValueError('start and end of spectrum need to be a length')
spectrum_config_dict = {}
spectrum_config_dict['start'] = spectrum_list[0]
spectrum_config_dict['end'] = spectrum_list[1]
spectrum_config_dict['bins'] = spectrum_list[2]
spectrum_frequency = quantity_linspace(
spectrum_config_dict['end'].to('Hz', u.spectral()),
spectrum_config_dict['start'].to('Hz', u.spectral()),
num=spectrum_config_dict['bins'] + 1)
spectrum_config_dict['frequency'] = spectrum_frequency
return spectrum_config_dict
def from_config(cls, config):
"""
Create a new MontecarloRunner instance from a Configuration object.
Parameters
----------
config : tardis.io.config_reader.Configuration
Returns
-------
MontecarloRunner
"""
if config.plasma.disable_electron_scattering:
logger.warn('Disabling electron scattering - this is not physical')
sigma_thomson = 1e-200 / (u.cm ** 2)
else:
logger.debug("Electron scattering switched on")
sigma_thomson = 6.652486e-25 / (u.cm ** 2)
spectrum_frequency = quantity_linspace(
config.spectrum.stop.to('Hz', u.spectral()),
config.spectrum.start.to('Hz', u.spectral()),
num=config.spectrum.num + 1)
return cls(seed=config.montecarlo.seed,
spectrum_frequency=spectrum_frequency,
virtual_spectrum_range=config.montecarlo.virtual_spectrum_range,
sigma_thomson=sigma_thomson,
enable_reflective_inner_boundary=config.montecarlo.enable_reflective_inner_boundary,
inner_boundary_albedo=config.montecarlo.inner_boundary_albedo,
line_interaction_type=config.plasma.line_interaction_type,
distance=config.supernova.get('distance', None))
def kappa(nu, nu0=271.1*u.GHz, kappa0=0.0114*u.cm**2*u.g**-1, beta=1.75):
"""
Compute the opacity $\kappa$ given a reference frequency (or wavelength)
and a power law governing the opacity as a fuction of frequency:
$$ \kappa = \kappa_0 \left(\\frac{\\nu}{\\nu_0}\\right)^{\\beta} $$
The default kappa=0.0114 at 271.1 GHz comes from extrapolating the
Ossenkopf & Henning 1994 opacities for the thin-ice-mantle, 10^6 year model
anchored at 1.0 mm with an assumed beta of 1.75.
Parameters
----------
nu: astropy.Quantity [u.spectral() equivalent]
The frequency at which to evaluate kappa
nu0: astropy.Quantity [u.spectral() equivalent]
The reference frequency at which $\kappa$ is defined
kappa0: astropy.Quantity [cm^2/g]
The dust opacity per gram of H2 along the line of sight. Because of
the H2 conversion, this factor implicitly includes a dust to gas ratio
(usually assumed 100)
beta: float
The power-law index governing kappa as a function of nu
"""
return (kappa0*(nu.to(u.GHz,u.spectral())/nu0.to(u.GHz,u.spectral()))**(beta)).to(u.cm**2/u.g)
def to_hdf5_group(self, group, name):
self.check_all_set()
# Get spectral coordinate in Hz and transmision in fractional terms
nu = self.spectral_coord.to(u.Hz, equivalencies=u.spectral()).value
tr = self.transmission.to(u.one).value
# Sort in order of increasing Hz
order = np.argsort(nu)
nu = nu[order]
tr = tr[order]
# Get other parameters for the normalization
nu0 = self.central_spectral_coord.to(u.Hz, equivalencies=u.spectral()).value
alpha = self.alpha
beta = self._beta
# Here we normalize the filter before passing it to Hyperion
tr_norm = tr / nu ** (1 + beta) / nu0 ** alpha / integrate(nu, tr / nu ** (1.0 + alpha + beta))
# Now multiply by nu so that Hyperion returns nu * Fnu
tr_norm *= nu
dset = group.create_dataset(
name, data=np.array(list(zip(nu, tr, tr_norm)), dtype=[("nu", float), ("tr", float), ("tn", float)])
)
dset.attrs["name"] = np.string_(self.name)
dset.attrs["alpha"] = self.alpha
dset.attrs["beta"] = self._beta
dset.attrs["nu0"] = self.central_spectral_coord.to(u.Hz, equivalencies=u.spectral()).value
def __readCDMS(self):
'''
Read data from CDMS line list catalogs for a specific molecule.
'''
data = DataIO.readFile(self.fn,\
replace_spaces=0)
print 'Reading data from CDMS database for'
print self.fn
#-- If the uncertainties are negative, change the unit of min/max to
# cm-1
uncertainties = [float(line[13:21]) for line in data]
if min(uncertainties) < 0 and max(uncertainties) == 0:
self.x_min = self.x_min.to(1./u.cm,equivalencies=u.spectral())
self.x_max = self.x_max.to(1./u.cm,equivalencies=u.spectral())
elif min(uncertainties) < 0 and max(uncertainties) > 0:
raise ValueError('Uncertainties in CDMS input file for ' + \
'file %s are ambiguous.'\
%self.fn)
data = self.__parseCatalog(data)
#-- If unit was changed, change the f values to MHz, the default unit
rcm = u.Unit("1 / cm")
if self.x_min.unit == rcm:
data = sorted([[(entry*rcm).to(u.MHz,equivalencies=u.spectral())
if not i else entry
for i,entry in enumerate(line)]
for line in data])
self.line_list = data
def _xunit_is_equivalent(self,unit):
from .datasource import UtilsUnits as Utils
from astropy.units import spectral
assert not Utils.is_dimensionless(self.xunit)
_a = Utils.are_equivalents(unit, self._xunit_kind, spectral())
_b = Utils.are_equivalents(unit, self.xunit, spectral())
return _a and _b
def parse_spectral_bin(spectral_bin_boundary_1, spectral_bin_boundary_2):
spectral_bin_boundary_1 = parse_quantity(spectral_bin_boundary_1).to('Angstrom', u.spectral())
spectral_bin_boundary_2 = parse_quantity(spectral_bin_boundary_2).to('Angstrom', u.spectral())
spectrum_start_wavelength = min(spectral_bin_boundary_1, spectral_bin_boundary_2)
spectrum_end_wavelength = max(spectral_bin_boundary_1, spectral_bin_boundary_2)
return spectrum_start_wavelength, spectrum_end_wavelength
def cdelt_derivative(crval, cdelt, intype, outtype, linear=False, rest=None):
if intype == outtype:
return cdelt
elif set((outtype, intype)) == set(("length", "frequency")):
# Symmetric equations!
return (-constants.c / crval ** 2 * cdelt).to(PHYS_UNIT_DICT[outtype])
elif outtype in ("frequency", "length") and intype == "speed":
if linear:
numer = cdelt * rest.to(PHYS_UNIT_DICT[outtype], u.spectral())
denom = constants.c
else:
numer = cdelt * constants.c * rest.to(PHYS_UNIT_DICT[outtype], u.spectral())
denom = (constants.c + crval) * (constants.c ** 2 - crval ** 2) ** 0.5
if outtype == "frequency":
return (-numer / denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
else:
return (numer / denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
elif outtype == "speed" and intype in ("frequency", "length"):
if linear:
numer = cdelt * constants.c
denom = rest.to(PHYS_UNIT_DICT[intype], u.spectral())
else:
numer = 4 * constants.c * crval * rest.to(crval.unit, u.spectral()) ** 2 * cdelt
denom = (crval ** 2 + rest.to(crval.unit, u.spectral()) ** 2) ** 2
if intype == "frequency":
return (-numer / denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
else:
return (numer / denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
elif intype == "air wavelength":
raise TypeError("Air wavelength should be converted to vacuum earlier.")
elif outtype == "air wavelength":
raise TypeError("Conversion to air wavelength not supported.")
else:
raise ValueError("Invalid in/out frames")
def cdelt_derivative(crval, cdelt, intype, outtype, linear=False, rest=None):
if intype == outtype:
return cdelt
elif set((outtype,intype)) == set(('length','frequency')):
# Symmetric equations!
return (-constants.c / crval**2 * cdelt).to(PHYS_UNIT_DICT[outtype])
elif outtype in ('frequency','length') and intype == 'speed':
if linear:
numer = cdelt * rest.to(PHYS_UNIT_DICT[outtype], u.spectral())
denom = constants.c
else:
numer = cdelt * constants.c * rest.to(PHYS_UNIT_DICT[outtype], u.spectral())
denom = (constants.c + crval)*(constants.c**2 - crval**2)**0.5
if outtype == 'frequency':
return (-numer/denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
else:
return (numer/denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
elif outtype == 'speed' and intype in ('frequency','length'):
if linear:
numer = cdelt * constants.c
denom = rest.to(PHYS_UNIT_DICT[intype], u.spectral())
else:
numer = 4 * constants.c * crval * rest.to(crval.unit, u.spectral())**2 * cdelt
denom = (crval**2 + rest.to(crval.unit, u.spectral())**2)**2
if intype == 'frequency':
return (-numer/denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
else:
return (numer/denom).to(PHYS_UNIT_DICT[outtype], u.spectral())
else:
raise ValueError("Invalid in/out frames")
def bbfunc(wavelengths, temperature):
"""Planck law for blackbody radiation in PHOTLAM per steradian.
.. warning::
Data points where overflow or underflow occurs will be set
to zeroes.
Parameters
----------
wavelengths : array_like or `~astropy.units.quantity.Quantity`
Wavelength values. If not a Quantity, assumed to be in Angstrom.
temperature : float or `~astropy.units.quantity.Quantity`
Blackbody temperature. If not a Quantity, assumed to be in Kelvin.
Returns
-------
fluxes : `~astropy.units.quantity.Quantity`
Blackbody radiation in PHOTLAM per steradian.
"""
# Silence Numpy
old_np_err_cfg = np.seterr(all='ignore')
# Calculations must use Angstrom
wavelengths = units.validate_quantity(
wavelengths, u.AA, equivalencies=u.spectral()).astype(np.float64)
# Calculations must use Kelvin
temperature = units.validate_quantity(temperature, u.K).astype(np.float64)
x = wavelengths * temperature
# Catch division by zero
mask = x > 0
x = np.where(mask, units.HC / (const.k_B.cgs * x), 0.0)
# Catch overflow/underflow
mask = (x >= _VERY_SMALL) & (x < _VERY_LARGE)
factor = np.where(mask, 1.0 / np.expm1(x), 0.0)
# Convert FNU to PHOTLAM
freq = u.Quantity(np.where(
factor, wavelengths.to(u.Hz, equivalencies=u.spectral()), 0.0), u.Hz)
bb_nu = 2.0 * const.h * factor * freq * freq * freq / const.c ** 2
bb_lam = np.where(
factor, units.FNU.to(units.PHOTLAM, bb_nu.cgs.value,
equivalencies=u.spectral_density(wavelengths)),
0.0)
# Restore Numpy settings
dummy = np.seterr(**old_np_err_cfg)
return u.Quantity(bb_lam, unit=units.PHOTLAM/u.sr)
def _(attr, results):
return set(
it for it in results
if
it.wave.wavemax is not None
and
attr.min <= it.wave.wavemax.to(u.angstrom, equivalencies=u.spectral())
and
it.wave.wavemin is not None
and
attr.max >= it.wave.wavemin.to(u.angstrom, equivalencies=u.spectral())
)
def shift_rv(self, rv):
'''Shift spectrum by rv
Parameters
----------
rv : :class:`~astropy.quantity.Quantity`
radial velocity (positive value will red-shift the spectrum, negative
value will blue-shift the spectrum)
'''
self[self.dispersion] = (self.disp.to(u.m, equivalencies=u.spectral()) * (
1.*u.dimensionless_unscaled+rv/const.c)).to(
self.disp.unit, equivalencies=u.spectral()).value
def test_broadband(self, tmpdir):
np.random.seed(12345)
from ..filter import Filter
f1_wav = np.linspace(5., 1., 100) * u.micron
f1 = Filter()
f1.name = 'alice'
f1.central_wavelength = 7. * u.micron
f1.nu = f1_wav.to(u.Hz, equivalencies=u.spectral())
f1.response = np.random.random(100)
f1.normalize()
f2_wav = np.linspace(15., 10., 100) * u.micron
f2 = Filter()
f2.name = 'bob'
f2.central_wavelength = 12. * u.micron
f2.nu = f2_wav.to(u.Hz, equivalencies=u.spectral())
f2.response = np.random.random(100)
f2.normalize()
f3_wav = np.linspace(25., 15., 100) * u.micron
f3 = Filter()
f3.name = 'eve'
f3.central_wavelength = 20. * u.micron
f3.nu = f3_wav.to(u.Hz, equivalencies=u.spectral())
f3.response = np.random.random(100)
f3.normalize()
from ..convolve import convolve_model_dir
convolve_model_dir(self.tmpdir, filters=[f1, f2, f3])
from ..fit import fit
data_file = tmpdir.join('data').strpath
open(data_file, 'w').write(DATA.strip())
output_file = tmpdir.join('output').strpath
fit(data_file, ['bob', 'alice', 'eve'], [1., 3., 3.] * u.arcsec, self.tmpdir, output_file,
extinction_law=self.extinction,
distance_range=[1., 2.] * u.kpc,
av_range=[0., 0.1],
output_format=('F', 3.),
output_convolved=False)
self._postprocess(output_file, tmpdir)
def nu_bins(self):
"""frequency grid for the opacity evaluation"""
if self._nu_bins is None:
nu_max = self.lam_min.to("Hz", equivalencies=units.spectral())
nu_min = self.lam_max.to("Hz", equivalencies=units.spectral())
if self.bin_scaling == "log":
nu_bins = (np.logspace(np.log10(nu_min.value),
np.log10(nu_max.value), self.nbins+1) *
units.Hz)
elif self.bin_scaling == "linear":
nu_bins = np.linspace(nu_min, nu_max, self.nbins+1)
self._nu_bins = nu_bins
return self._nu_bins
def write_input(temperature=10, column=1e12, collider_densities={'H2':1},
bw=0.01, tbg=2.73, species='co', velocity_gradient=1.0, minfreq=1,
maxfreq=10, delete_tempfile=True):
"""
Write radex.inp file parameters
Parameters
----------
temperature : float
Kinetic temperature (K)
collider_densities : dict
Collider names and their number densities
column : float
column density of the molecule
species : str
Name of the molecule (specifically, the prefix for the file name, e.g.
for "co.dat", species='co'). Case sensitive!
tbg : float
Temperature of the background radiation (e.g. CMB)
velocity_gradient : float
Velocity gradient per pc in km/s
"""
if hasattr(minfreq, 'unit'):
minfreq = unitless(minfreq.to('GHz',u.spectral()))
if hasattr(maxfreq, 'unit'):
maxfreq = unitless(maxfreq.to('GHz',u.spectral()))
infile = tempfile.NamedTemporaryFile(mode='w', delete=delete_tempfile)
outfile = tempfile.NamedTemporaryFile(mode='w', delete=delete_tempfile)
infile.write(species+'.dat\n')
infile.write(outfile.name+'\n')
infile.write(str(minfreq)+' '+str(maxfreq)+'\n')
infile.write(str(temperature)+'\n')
# RADEX doesn't allow densities < 1e-3
for k in collider_densities.keys():
if collider_densities[k] < 1e-3:
collider_densities.pop(k)
infile.write('%s\n' % len(collider_densities))
for name,dens in collider_densities.iteritems():
infile.write('%s\n' % name)
infile.write(str(dens)+'\n')
infile.write(str(tbg)+'\n')
infile.write(str(column)+'\n')
infile.write(str(velocity_gradient)+'\n')
# end the input file
infile.write('0\n')
infile.flush()
return infile,outfile
def parse_supernova_section(supernova_dict):
"""
Parse the supernova section
Parameters
----------
supernova_dict: dict
YAML parsed supernova dict
Returns
-------
config_dict: dict
"""
config_dict = {}
# parse luminosity
luminosity_value, luminosity_unit = supernova_dict["luminosity_requested"].strip().split()
if luminosity_unit == "log_lsun":
config_dict["luminosity_requested"] = (
10 ** (float(luminosity_value) + np.log10(constants.L_sun.cgs.value)) * u.erg / u.s
)
else:
config_dict["luminosity_requested"] = (float(luminosity_value) * u.Unit(luminosity_unit)).to("erg/s")
config_dict["time_explosion"] = parse_quantity(supernova_dict["time_explosion"]).to("s")
if "distance" in supernova_dict:
config_dict["distance"] = parse_quantity(supernova_dict["distance"])
else:
config_dict["distance"] = None
if "luminosity_wavelength_start" in supernova_dict:
config_dict["luminosity_nu_end"] = parse_quantity(supernova_dict["luminosity_wavelength_start"]).to(
"Hz", u.spectral()
)
else:
config_dict["luminosity_nu_end"] = np.inf * u.Hz
if "luminosity_wavelength_end" in supernova_dict:
config_dict["luminosity_nu_start"] = parse_quantity(supernova_dict["luminosity_wavelength_end"]).to(
"Hz", u.spectral()
)
else:
config_dict["luminosity_nu_start"] = 0.0 * u.Hz
return config_dict
def test_spectral4(in_val, in_unit):
"""Wave number conversion w.r.t. wavelength, freq, and energy."""
# Spectroscopic and angular
out_units = [u.micron ** -1, u.radian / u.micron]
answers = [[1e+5, 2.0, 1.0], [6.28318531e+05, 12.5663706, 6.28318531]]
for out_unit, ans in zip(out_units, answers):
# Forward
a = in_unit.to(out_unit, in_val, u.spectral())
assert_allclose(a, ans)
# Backward
b = out_unit.to(in_unit, ans, u.spectral())
assert_allclose(b, in_val)
def test_input_units_equivalencies(self):
self.model._input_units = {'a': u.micron}
with pytest.raises(UnitsError) as exc:
self.model(3 * u.PHz, 3)
assert exc.value.args[0] == ("MyTestModel: Units of input 'a', PHz (frequency), could "
"not be converted to required input units of "
"micron (length)")
self.model.input_units_equivalencies = {'a': u.spectral()}
assert_quantity_allclose(self.model(3 * u.PHz, 3),
3 * (3 * u.PHz).to(u.micron, equivalencies=u.spectral()))
def _get_range_from_textfields(self, min_text, max_text, linelist_units, plot_units):
amin = amax = None
if min_text.hasAcceptableInput() and max_text.hasAcceptableInput():
amin = float(min_text.text())
amax = float(max_text.text())
amin = Quantity(amin, plot_units)
amax = Quantity(amax, plot_units)
amin = amin.to(linelist_units, equivalencies=u.spectral())
amax = amax.to(linelist_units, equivalencies=u.spectral())
return (amin, amax)
def convert_ha(self):
"""
This function ...
:return:
"""
# What I thought the unit conversion should be:
# Conversion from erg / [s * cm2] (per pixel2) to erg / [s * cm2 * micron] (per pixel2) --> divide by eff. bandwidth
#self.conversion_factor *= 1.0 / self.image.filter.effective_bandwidth()
# Conversion from erg / [s * cm2 * micron] (per pixel2) to erg / [s * cm2 * Hz] (per pixel2)
#self.conversion_factor *= self.spectral_factor_micron_to_hz(self.image.wavelength)
# What Ilse says it should be:
# Get the frequency of Ha
frequency = self.image.wavelength.to("Hz", equivalencies=spectral())
# Conversion from erg / [s * cm2] (per pixel2) to erg / [s * cm2 * Hz] (per pixel2)
self.conversion_factor *= 1.0 / frequency.value
# Conversion from erg / [s * cm2 * Hz] per pixel2 to the target unit (MJy / sr)
self.convert_from_ergscmhz()
# Correct for contribution of NII (Bendo et. al 2015) NII/Halpha = 0.55 for M81 => divide by a factor of 1.55
self.conversion_factor *= 1.0 / 1.55
def test_with_spectral_unit(self, name, masktype):
cube, data = cube_and_raw(name + '.fits')
cube_freq = cube.with_spectral_unit(u.Hz)
if masktype == BooleanArrayMask:
mask = BooleanArrayMask(data>0, wcs=cube._wcs)
elif masktype == LazyMask:
mask = LazyMask(lambda x: x>0, cube=cube)
elif masktype == FunctionMask:
mask = FunctionMask(lambda x: x>0)
elif masktype == CompositeMask:
mask1 = FunctionMask(lambda x: x>0)
mask2 = LazyMask(lambda x: x>0, cube)
mask = CompositeMask(mask1, mask2)
cube2 = cube.with_mask(mask)
cube_masked_freq = cube2.with_spectral_unit(u.Hz)
assert cube_freq._wcs.wcs.ctype[cube_freq._wcs.wcs.spec] == 'FREQ-W2F'
assert cube_masked_freq._wcs.wcs.ctype[cube_masked_freq._wcs.wcs.spec] == 'FREQ-W2F'
assert cube_masked_freq._mask._wcs.wcs.ctype[cube_masked_freq._mask._wcs.wcs.spec] == 'FREQ-W2F'
# values taken from header
rest = 1.42040571841E+09*u.Hz
crval = -3.21214698632E+05*u.m/u.s
outcv = crval.to(u.m, u.doppler_optical(rest)).to(u.Hz, u.spectral())
assert_allclose(cube_freq._wcs.wcs.crval[cube_freq._wcs.wcs.spec],
outcv.to(u.Hz).value)
assert_allclose(cube_masked_freq._wcs.wcs.crval[cube_masked_freq._wcs.wcs.spec],
outcv.to(u.Hz).value)
assert_allclose(cube_masked_freq._mask._wcs.wcs.crval[cube_masked_freq._mask._wcs.wcs.spec],
outcv.to(u.Hz).value)
def calculate_spectrum(self):
if self.tardis_config.sn_distance is None:
logger.info('Distance to supernova not selected assuming 10 pc for calculation of spectra')
distance = units.Quantity(10, 'pc').to('cm').value
else:
distance = self.tardis_config.sn_distance
self.spec_flux_nu = np.histogram(self.montecarlo_nu[self.montecarlo_nu > 0],
weights=self.montecarlo_energies[self.montecarlo_energies > 0],
bins=self.spec_nu_bins)[0]
flux_scale = (self.time_of_simulation * (self.spec_nu[1] - self.spec_nu[0]) * (4 * np.pi * distance ** 2))
self.spec_flux_nu /= flux_scale
self.spec_virtual_flux_nu /= flux_scale
self.spec_reabsorbed_nu = \
np.histogram(self.montecarlo_nu[self.montecarlo_nu < 0],
weights=self.montecarlo_energies[self.montecarlo_nu < 0], bins=self.spec_nu_bins)[0]
self.spec_reabsorbed_nu /= flux_scale
self.spec_angstrom = units.Unit('Hz').to('angstrom', self.spec_nu, units.spectral())
self.spec_flux_angstrom = (self.spec_flux_nu * self.spec_nu ** 2 / constants.c.cgs.value / 1e8)
self.spec_reabsorbed_angstrom = (self.spec_reabsorbed_nu * self.spec_nu ** 2 / constants.c.cgs.value / 1e8)
self.spec_virtual_flux_angstrom = (self.spec_virtual_flux_nu * self.spec_nu ** 2 / constants.c.cgs.value / 1e8)
def __getitem__(self, item):
"""
Override the class indexer. We do this here because there are two cases
for slicing on a ``Spectrum1D``:
1.) When the flux is one dimensional, indexing represents a single
flux value at a particular spectral axis bin, and returns a new
``Spectrum1D`` where all attributes are sliced.
2.) When flux is multi-dimensional (i.e. several fluxes over the
same spectral axis), indexing returns a new ``Spectrum1D`` with
the sliced flux range and a deep copy of all other attributes.
The first case is handled by the parent class, while the second is
handled here.
"""
if self.flux.ndim > 1 or (type(item) == tuple and item[0] == Ellipsis):
if type(item) == tuple:
if len(item) == len(self.flux.shape) or item[0] == Ellipsis:
spec_item = item[-1]
if not isinstance(spec_item, slice):
if isinstance(item, u.Quantity):
raise ValueError(
"Indexing on single spectral axis "
"values is not currently allowed, "
"please use a slice.")
spec_item = slice(spec_item, spec_item + 1, None)
item = item[:-1] + (spec_item, )
else:
# Slicing on less than the full number of axes means we want
# to keep the whole spectral axis
spec_item = slice(None, None, None)
elif isinstance(item,
slice) and (isinstance(item.start, u.Quantity)
or isinstance(item.stop, u.Quantity)):
# We only allow slicing with world coordinates along the spectral
# axis for now
for attr in ("start", "stop"):
if getattr(item, attr) is None:
continue
if not getattr(item, attr).unit.is_equivalent(
u.AA, equivalencies=u.spectral()):
raise ValueError(
"Slicing with world coordinates is only"
" enabled for spectral coordinates.")
break
spec_item = item
else:
# Slicing with a single integer or slice uses the leading axis,
# so we keep the whole spectral axis, which is last
spec_item = slice(None, None, None)
if (isinstance(spec_item.start, u.Quantity)
or isinstance(spec_item.stop, u.Quantity)):
temp_spec = self._spectral_slice(spec_item)
if spec_item is item:
return temp_spec
else:
# Drop the spectral axis slice and perform only the spatial part
return temp_spec[item[:-1]]
if "original_wcs" not in self.meta:
new_meta = deepcopy(self.meta)
new_meta["original_wcs"] = deepcopy(self.wcs)
else:
new_meta = deepcopy(self.meta)
return self._copy(
flux=self.flux[item],
spectral_axis=self.spectral_axis[spec_item],
uncertainty=self.uncertainty[item]
if self.uncertainty is not None else None,
mask=self.mask[item] if self.mask is not None else None,
meta=new_meta,
wcs=None)
if not isinstance(item, slice):
if isinstance(item, u.Quantity):
raise ValueError(
"Indexing on a single spectral axis value is not"
" currently allowed, please use a slice.")
# Handle tuple slice as input by NDCube crop method
elif isinstance(item, tuple):
if len(item) == 1 and isinstance(item[0], slice):
item = item[0]
else:
raise ValueError(f"Unclear how to slice with tuple {item}")
else:
item = slice(item, item + 1, None)
elif (isinstance(item.start, u.Quantity)
or isinstance(item.stop, u.Quantity)):
return self._spectral_slice(item)
tmp_spec = super().__getitem__(item)
# TODO: this is a workaround until we figure out how to deal with non-
# strictly ascending spectral axes. Currently, the wcs is created from
# a spectral axis array by converting to a length physical type. On
# a regular slicing operation, the wcs is handed back to the
# initializer and a new spectral axis is created. This would then also
# be in length units, which may not be the units used initially. So,
# we create a new ``Spectrum1D`` that includes the sliced spectral
# axis. This means that a new wcs object will be created with the
# appropriate unit translation handling.
if "original_wcs" not in self.meta:
new_meta = deepcopy(self.meta)
new_meta["original_wcs"] = deepcopy(self.wcs)
else:
new_meta = deepcopy(self.meta)
return tmp_spec._copy(spectral_axis=self.spectral_axis[item],
wcs=None,
meta=new_meta)
def __init__(self,
flux=None,
spectral_axis=None,
wcs=None,
velocity_convention=None,
rest_value=None,
redshift=None,
radial_velocity=None,
bin_specification=None,
**kwargs):
# Check for pre-defined entries in the kwargs dictionary.
unknown_kwargs = set(kwargs).difference({
'data', 'unit', 'uncertainty', 'meta', 'mask', 'copy',
'extra_coords'
})
if len(unknown_kwargs) > 0:
raise ValueError("Initializer contains unknown arguments(s): {}."
"".format(', '.join(map(str, unknown_kwargs))))
# If the flux (data) argument is already a Spectrum1D (as it would
# be for internal arithmetic operations), avoid setup entirely.
if isinstance(flux, Spectrum1D):
super().__init__(flux)
return
# Handle initializing from NDCube objects
elif isinstance(flux, NDCube):
if flux.unit is None:
raise ValueError("Input NDCube missing unit parameter")
# Change the flux array from bare ndarray to a Quantity
q_flux = flux.data << u.Unit(flux.unit)
self.__init__(flux=q_flux,
wcs=flux.wcs,
mask=flux.mask,
uncertainty=flux.uncertainty)
return
# If the mask kwarg is not passed to the constructor, but the flux array
# contains NaNs, add the NaN locations to the mask.
if "mask" not in kwargs and flux is not None:
nan_mask = np.isnan(flux)
if nan_mask.any():
if hasattr(self, "mask"):
kwargs["mask"] = np.logical_or(nan_mask, self.mask)
else:
kwargs["mask"] = nan_mask.copy()
del nan_mask
# Ensure that the flux argument is an astropy quantity
if flux is not None:
if not isinstance(flux, u.Quantity):
raise ValueError("Flux must be a `Quantity` object.")
elif flux.isscalar:
flux = u.Quantity([flux])
# Ensure that only one or neither of these parameters is set
if redshift is not None and radial_velocity is not None:
raise ValueError("Cannot set both radial_velocity and redshift at "
"the same time.")
# In cases of slicing, new objects will be initialized with `data`
# instead of ``flux``. Ensure we grab the `data` argument.
if flux is None and 'data' in kwargs:
flux = kwargs.pop('data')
# Ensure that the unit information codified in the quantity object is
# the One True Unit.
kwargs.setdefault(
'unit',
flux.unit if isinstance(flux, u.Quantity) else kwargs.get('unit'))
# In the case where the arithmetic operation is being performed with
# a single float, int, or array object, just go ahead and ignore wcs
# requirements
if (not isinstance(flux, u.Quantity) or isinstance(flux, float)
or isinstance(flux, int)) and np.ndim(flux) == 0:
super(Spectrum1D, self).__init__(data=flux, wcs=wcs, **kwargs)
return
if rest_value is None:
if hasattr(wcs, 'rest_frequency') and wcs.rest_frequency != 0:
rest_value = wcs.rest_frequency * u.Hz
elif hasattr(wcs, 'rest_wavelength') and wcs.rest_wavelength != 0:
rest_value = wcs.rest_wavelength * u.AA
elif hasattr(wcs, 'wcs') and hasattr(
wcs.wcs, 'restfrq') and wcs.wcs.restfrq > 0:
rest_value = wcs.wcs.restfrq * u.Hz
elif hasattr(wcs, 'wcs') and hasattr(
wcs.wcs, 'restwav') and wcs.wcs.restwav > 0:
rest_value = wcs.wcs.restwav * u.m
else:
rest_value = None
else:
if not isinstance(rest_value, u.Quantity):
warnings.warn(
"No unit information provided with rest value. "
f"Assuming units of spectral axis ('{spectral_axis.unit}')."
)
rest_value = u.Quantity(rest_value, spectral_axis.unit)
elif not rest_value.unit.is_equivalent(u.AA,
equivalencies=u.spectral()):
raise u.UnitsError("Rest value must be "
"energy/wavelength/frequency equivalent.")
# If flux and spectral axis are both specified, check that their lengths
# match or are off by one (implying the spectral axis stores bin edges)
if flux is not None and spectral_axis is not None:
if spectral_axis.shape[0] == flux.shape[-1]:
if bin_specification == "edges":
raise ValueError(
"A spectral axis input as bin edges"
"must have length one greater than the flux axis")
bin_specification = "centers"
elif spectral_axis.shape[0] == flux.shape[-1] + 1:
if bin_specification == "centers":
raise ValueError(
"A spectral axis input as bin centers"
"must be the same length as the flux axis")
bin_specification = "edges"
else:
raise ValueError(
"Spectral axis length ({}) must be the same size or one "
"greater (if specifying bin edges) than that of the last "
"flux axis ({})".format(spectral_axis.shape[0],
flux.shape[-1]))
# If a WCS is provided, check that the spectral axis is last and reorder
# the arrays if not
if wcs is not None and hasattr(wcs, "naxis"):
if wcs.naxis > 1:
temp_axes = []
phys_axes = wcs.world_axis_physical_types
for i in range(len(phys_axes)):
if phys_axes[i] is None:
continue
if phys_axes[i][0:2] == "em" or phys_axes[i][
0:5] == "spect":
temp_axes.append(i)
if len(temp_axes) != 1:
raise ValueError(
"Input WCS must have exactly one axis with "
"spectral units, found {}".format(len(temp_axes)))
# Due to FITS conventions, a WCS with spectral axis first corresponds
# to a flux array with spectral axis last.
if temp_axes[0] != 0:
warnings.warn(
"Input WCS indicates that the spectral axis is not"
" last. Reshaping arrays to put spectral axis last.")
wcs = wcs.swapaxes(0, temp_axes[0])
if flux is not None:
flux = np.swapaxes(flux,
len(flux.shape) - temp_axes[0] - 1,
-1)
if "mask" in kwargs:
if kwargs["mask"] is not None:
kwargs["mask"] = np.swapaxes(
kwargs["mask"],
len(kwargs["mask"].shape) - temp_axes[0] - 1,
-1)
if "uncertainty" in kwargs:
if kwargs["uncertainty"] is not None:
if isinstance(kwargs["uncertainty"],
NDUncertainty):
# Account for Astropy uncertainty types
unc_len = len(
kwargs["uncertainty"].array.shape)
temp_unc = np.swapaxes(
kwargs["uncertainty"].array,
unc_len - temp_axes[0] - 1, -1)
if kwargs["uncertainty"].unit is not None:
temp_unc = temp_unc * u.Unit(
kwargs["uncertainty"].unit)
kwargs["uncertainty"] = type(
kwargs["uncertainty"])(temp_unc)
else:
kwargs["uncertainty"] = np.swapaxes(
kwargs["uncertainty"],
len(kwargs["uncertainty"].shape) -
temp_axes[0] - 1, -1)
# Attempt to parse the spectral axis. If none is given, try instead to
# parse a given wcs. This is put into a GWCS object to
# then be used behind-the-scenes for all specutils operations.
if spectral_axis is not None:
# Ensure that the spectral axis is an astropy Quantity
if not isinstance(spectral_axis, u.Quantity):
raise ValueError("Spectral axis must be a `Quantity` or "
"`SpectralAxis` object.")
# If spectral axis is provided as an astropy Quantity, convert it
# to a specutils SpectralAxis object.
if not isinstance(spectral_axis, SpectralAxis):
if spectral_axis.shape[0] == flux.shape[-1] + 1:
bin_specification = "edges"
else:
bin_specification = "centers"
self._spectral_axis = SpectralAxis(
spectral_axis,
redshift=redshift,
radial_velocity=radial_velocity,
doppler_rest=rest_value,
doppler_convention=velocity_convention,
bin_specification=bin_specification)
# If a SpectralAxis object is provided, we assume it doesn't need
# information from other keywords added
else:
for a in [radial_velocity, redshift]:
if a is not None:
raise ValueError("Cannot separately set redshift or "
"radial_velocity if a SpectralAxis "
"object is input to spectral_axis")
self._spectral_axis = spectral_axis
if wcs is None:
wcs = gwcs_from_array(self._spectral_axis)
elif wcs is None:
# If no spectral axis or wcs information is provided, initialize
# with an empty gwcs based on the flux.
size = flux.shape[-1] if not flux.isscalar else 1
wcs = gwcs_from_array(np.arange(size) * u.Unit(""))
super().__init__(
data=flux.value if isinstance(flux, u.Quantity) else flux,
wcs=wcs,
**kwargs)
# If no spectral_axis was provided, create a SpectralCoord based on
# the WCS
if spectral_axis is None:
# If the WCS doesn't have a spectral attribute, we assume it's the
# dummy GWCS we created or a solely spectral WCS
if hasattr(self.wcs, "spectral"):
# Handle generated 1D WCS that aren't set to spectral
if not self.wcs.is_spectral and self.wcs.naxis == 1:
spec_axis = self.wcs.pixel_to_world(
np.arange(self.flux.shape[-1]))
else:
spec_axis = self.wcs.spectral.pixel_to_world(
np.arange(self.flux.shape[-1]))
else:
spec_axis = self.wcs.pixel_to_world(
np.arange(self.flux.shape[-1]))
try:
if spec_axis.unit.is_equivalent(u.one):
spec_axis = spec_axis * u.pixel
except AttributeError:
raise AttributeError(f"spec_axis does not have unit: "
f"{type(spec_axis)} {spec_axis}")
self._spectral_axis = SpectralAxis(
spec_axis,
redshift=redshift,
radial_velocity=radial_velocity,
doppler_rest=rest_value,
doppler_convention=velocity_convention)
if hasattr(self, 'uncertainty') and self.uncertainty is not None:
if not flux.shape == self.uncertainty.array.shape:
raise ValueError(
"Flux axis ({}) and uncertainty ({}) shapes must be the "
"same.".format(flux.shape, self.uncertainty.array.shape))
def wavelength(self):
"""
The `spectral_axis` as a `~astropy.units.Quantity` in units of Angstroms
"""
return self.spectral_axis.to(u.AA, u.spectral())
def from_config(cls,
config,
packet_source=None,
virtual_packet_logging=False,
**kwargs):
"""
Create a new Simulation instance from a Configuration object.
Parameters
----------
config : tardis.io.config_reader.Configuration
**kwargs
Allow overriding some structures, such as model, plasma, atomic data
and the runner, instead of creating them from the configuration
object.
Returns
-------
Simulation
"""
# Allow overriding some config structures. This is useful in some
# unit tests, and could be extended in all the from_config classmethods.
if "model" in kwargs:
model = kwargs["model"]
else:
if hasattr(config, "csvy_model"):
model = Radial1DModel.from_csvy(config)
else:
model = Radial1DModel.from_config(config)
if "plasma" in kwargs:
plasma = kwargs["plasma"]
else:
plasma = assemble_plasma(config,
model,
atom_data=kwargs.get("atom_data", None))
if "runner" in kwargs:
if packet_source is not None:
raise ConfigurationError(
"Cannot specify packet_source and runner at the same time."
)
runner = kwargs["runner"]
else:
runner = MontecarloRunner.from_config(
config,
packet_source=packet_source,
virtual_packet_logging=virtual_packet_logging,
)
luminosity_nu_start = config.supernova.luminosity_wavelength_end.to(
u.Hz, u.spectral())
if u.isclose(config.supernova.luminosity_wavelength_start,
0 * u.angstrom):
luminosity_nu_end = np.inf * u.Hz
else:
luminosity_nu_end = (
const.c / config.supernova.luminosity_wavelength_start).to(
u.Hz)
last_no_of_packets = config.montecarlo.last_no_of_packets
if last_no_of_packets is None or last_no_of_packets < 0:
last_no_of_packets = config.montecarlo.no_of_packets
last_no_of_packets = int(last_no_of_packets)
return cls(
iterations=config.montecarlo.iterations,
model=model,
plasma=plasma,
runner=runner,
no_of_packets=int(config.montecarlo.no_of_packets),
no_of_virtual_packets=int(config.montecarlo.no_of_virtual_packets),
luminosity_nu_start=luminosity_nu_start,
luminosity_nu_end=luminosity_nu_end,
last_no_of_packets=last_no_of_packets,
luminosity_requested=config.supernova.luminosity_requested.cgs,
convergence_strategy=config.montecarlo.convergence_strategy,
nthreads=config.montecarlo.nthreads,
)
def test_validate_unit_exceptions():
"""Test that unit validation raises appropriate exceptions."""
with pytest.raises(exceptions.SynphotError):
x = units.validate_unit(10)
with pytest.raises(ValueError):
x = units.validate_unit('foo')
with pytest.raises(exceptions.SynphotError):
x = units.validate_wave_unit('Kelvin')
@pytest.mark.parametrize(
('in_val', 'out_u', 'eqv', 'ans'),
[(100.0, units.AREA, [], 100.0), (100.0 * units.AREA, u.m * u.m, [], 0.01),
(_wave_angstrom, u.micron**-1, u.spectral(), _wavenum_micron.value)])
def test_validate_quantity(in_val, out_u, eqv, ans):
"""Test quantity validation."""
result = units.validate_quantity(in_val, out_u, equivalencies=eqv)
np.testing.assert_allclose(result.value, ans)
assert result.unit == out_u
@pytest.mark.parametrize(('in_q', 'out_u', 'ans'),
[(_wave_angstrom, u.Hz, _freq),
(_freq, u.AA, _wave_angstrom),
(_wave_angstrom, u.micron**-1, _wavenum_micron),
(_wavenum_micron, u.AA, _wave_angstrom),
(_freq, u.micron**-1, _wavenum_micron),
(_wavenum_micron, u.Hz, _freq)])
def test_wave_conversion(in_q, out_u, ans):
if ppcat['Fpeak6cm_Becker'].unit is None:
ppcat['Fpeak6cm_Becker'].unit = u.mJy
if ppcat['Fpeak6cm_MAGPIS'].unit is None:
ppcat['Fpeak6cm_MAGPIS'].unit = u.Jy
for key in (70, 160, 250, 350, 500):
if ppcat[f'Fpeak{key}um'].unit is None:
ppcat[f'Fpeak{key}um'].unit = u.Jy / u.sr
ppcat['x_cen'].unit = u.deg
ppcat['y_cen'].unit = u.deg
ppcat['3mm20cmindex_THOR'] = np.log(
ppcat['MUSTANG_10as_peak'] /
(ppcat['Fpeak20cm_THOR'])) / np.log(
constants.mustang_central_frequency /
(20 * u.cm).to(u.GHz, u.spectral()))
ppcat['3mm20cmindex'] = np.log(
ppcat['MUSTANG_10as_peak'] /
(ppcat['Fpeak20cm'])) / np.log(
constants.mustang_central_frequency /
(20 * u.cm).to(u.GHz, u.spectral()))
ppcat['3mm1mmindex'] = np.log(
ppcat['MUSTANG_10as_peak'] /
(ppcat['Fint1100um_40as'] * 1.46)) / np.log(
constants.mustang_central_frequency / (271.1 * u.GHz))
ppcat['3mm6cmindex_MAGPIS'] = np.log(
ppcat['MUSTANG_10as_peak'] /
(ppcat['Fpeak6cm_MAGPIS'].quantity.to(u.Jy).value)
) / np.log(constants.mustang_central_frequency / (5 * u.GHz))
ppcat['3mm6cmindex_CORNISH'] = np.log(
ppcat['MUSTANG_10as_peak'] /
def main():
# setup and parse the command line
parser = initialize_parser()
args = parser.parse_args()
# read in the observed spectrum
# assumed to be astropy table compatibile and include units
specfile = args.spectrumfile
outputname = specfile.split(".")[0]
if not os.path.isfile(specfile):
pack_path = pkg_resources.resource_filename("pahfit", "data/")
test_specfile = "{}/{}".format(pack_path, specfile)
if os.path.isfile(test_specfile):
specfile = test_specfile
else:
raise ValueError(
"Input spectrumfile {} not found".format(specfile))
# get the table format (from extension of filename)
tformat = specfile.split(".")[-1]
if tformat == "ecsv":
tformat = "ascii.ecsv"
obs_spectrum = Table.read(specfile, format=tformat)
obs_x = obs_spectrum["wavelength"].to(u.micron, equivalencies=u.spectral())
obs_y = obs_spectrum["flux"].to(u.Jy,
equivalencies=u.spectral_density(obs_x))
obs_unc = obs_spectrum["sigma"].to(u.Jy,
equivalencies=u.spectral_density(obs_x))
# strip units as the observed spectrum is in the internal units
obs_x = obs_x.value
obs_y = obs_y.value
weights = 1.0 / obs_unc.value
# read in the pack file
packfile = args.packfile
if not os.path.isfile(packfile):
pack_path = pkg_resources.resource_filename("pahfit", "packs/")
test_packfile = "{}/{}".format(pack_path, packfile)
if os.path.isfile(test_packfile):
packfile = test_packfile
else:
raise ValueError("Input packfile {} not found".format(packfile))
pmodel = PAHFITBase(obs_x,
obs_y,
estimate_start=args.estimate_start,
filename=packfile)
# pick the fitter
fit = LevMarLSQFitter()
# fit
obs_fit = fit(
pmodel.model,
obs_x,
obs_y,
weights=weights,
maxiter=200,
epsilon=1e-10,
acc=1e-10,
)
print(fit.fit_info["message"])
# save results to fits file
pmodel.save(obs_fit, outputname, args.saveoutput)
# plot result
fontsize = 18
font = {"size": fontsize}
mpl.rc("font", **font)
mpl.rc("lines", linewidth=2)
mpl.rc("axes", linewidth=2)
mpl.rc("xtick.major", size=5, width=1)
mpl.rc("ytick.major", size=5, width=1)
mpl.rc("xtick.minor", size=3, width=1)
mpl.rc("ytick.minor", size=3, width=1)
fig, axs = plt.subplots(ncols=1,
nrows=2,
figsize=(15, 10),
gridspec_kw={'height_ratios': [3, 1]},
sharex=True)
pmodel.plot(axs,
obs_x,
obs_y,
obs_unc.value,
obs_fit,
scalefac_resid=args.scalefac_resid)
# use the whitespace better
fig.subplots_adjust(hspace=0)
# show
if args.showplot:
plt.show()
# save (always)
fig.savefig("{}.{}".format(outputname, args.savefig))
def evaluate(self, x, temperature, scale):
"""Evaluate the model.
Parameters
----------
x : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Frequency at which to compute the blackbody. If no units are given,
this defaults to Hz.
temperature : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Temperature of the blackbody. If no units are given, this defaults
to Kelvin.
scale : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Desired scale for the blackbody.
Returns
-------
y : number or ndarray
Blackbody spectrum. The units are determined from the units of
``scale``.
.. note::
Use `numpy.errstate` to suppress Numpy warnings, if desired.
.. warning::
Output values might contain ``nan`` and ``inf``.
Raises
------
ValueError
Invalid temperature.
ZeroDivisionError
Wavelength is zero (when converting to frequency).
"""
if not isinstance(temperature, u.Quantity):
in_temp = u.Quantity(temperature, u.K)
else:
in_temp = temperature
# Convert to units for calculations, also force double precision
with u.add_enabled_equivalencies(u.spectral() + u.temperature()):
freq = u.Quantity(x, u.Hz, dtype=np.float64)
temp = u.Quantity(in_temp, u.K)
# check the units of scale and setup the output units
bb_unit = u.erg / (u.cm ** 2 * u.s * u.Hz * u.sr) # default unit
# use the scale that was used at initialization for determining the units to return
# to support returning the right units when fitting where units are stripped
if hasattr(self.scale, "unit") and self.scale.unit is not None:
# check that the units on scale are covertable to surface brightness units
if not self.scale.unit.is_equivalent(bb_unit, u.spectral_density(x)):
raise ValueError(
f"scale units not surface brightness: {self.scale.unit}"
)
# use the scale passed to get the value for scaling
if hasattr(scale, "unit"):
mult_scale = scale.value
else:
mult_scale = scale
bb_unit = self.scale.unit
else:
mult_scale = scale
# Check if input values are physically possible
if np.any(temp < 0):
raise ValueError(f"Temperature should be positive: {temp}")
if not np.all(np.isfinite(freq)) or np.any(freq <= 0):
warnings.warn(
"Input contains invalid wavelength/frequency value(s)",
AstropyUserWarning,
)
log_boltz = const.h * freq / (const.k_B * temp)
boltzm1 = np.expm1(log_boltz)
# Calculate blackbody flux
bb_nu = 2.0 * const.h * freq ** 3 / (const.c ** 2 * boltzm1) / u.sr
y = mult_scale * bb_nu.to(bb_unit, u.spectral_density(freq))
# If the temperature parameter has no unit, we should return a unitless
# value. This occurs for instance during fitting, since we drop the
# units temporarily.
if hasattr(temperature, "unit"):
return y
else:
return y.value
def _new_spectral_wcs(self, unit, velocity_convention=None,
rest_value=None):
"""
Returns a new WCS with a different Spectral Axis unit
Parameters
----------
unit : :class:`~astropy.units.Unit`
Any valid spectral unit: velocity, (wave)length, or frequency.
Only vacuum units are supported.
velocity_convention : 'relativistic', 'radio', or 'optical'
The velocity convention to use for the output velocity axis.
Required if the output type is velocity. This can be either one
of the above strings, or an `astropy.units` equivalency.
rest_value : :class:`~astropy.units.Quantity`
A rest wavelength or frequency with appropriate units. Required if
output type is velocity. The cube's WCS should include this
already if the *input* type is velocity, but the WCS's rest
wavelength/frequency can be overridden with this parameter.
.. note: This must be the rest frequency/wavelength *in vacuum*,
even if your cube has air wavelength units
"""
from .spectral_axis import (convert_spectral_axis,
determine_ctype_from_vconv)
# Allow string specification of units, for example
if not isinstance(unit, u.Unit):
unit = u.Unit(unit)
# Velocity conventions: required for frq <-> velo
# convert_spectral_axis will handle the case of no velocity
# convention specified & one is required
if velocity_convention in DOPPLER_CONVENTIONS:
velocity_convention = DOPPLER_CONVENTIONS[velocity_convention]
elif (velocity_convention is not None and
velocity_convention not in DOPPLER_CONVENTIONS.values()):
raise ValueError("Velocity convention must be radio, optical, "
"or relativistic.")
# If rest value is specified, it must be a quantity
if (rest_value is not None and
(not hasattr(rest_value, 'unit') or
not rest_value.unit.is_equivalent(u.m, u.spectral()))):
raise ValueError("Rest value must be specified as an astropy "
"quantity with spectral equivalence.")
# Shorter versions to keep lines under 80
ctype_from_vconv = determine_ctype_from_vconv
meta = self._meta.copy()
if 'Original Unit' not in self._meta:
meta['Original Unit'] = self._wcs.wcs.cunit[self._wcs.wcs.spec]
meta['Original Type'] = self._wcs.wcs.ctype[self._wcs.wcs.spec]
out_ctype = ctype_from_vconv(self._wcs.wcs.ctype[self._wcs.wcs.spec],
unit,
velocity_convention=velocity_convention)
newwcs = convert_spectral_axis(self._wcs, unit, out_ctype,
rest_value=rest_value)
newwcs.wcs.set()
return newwcs, meta
class BlackBody(Fittable1DModel):
"""
Blackbody model using the Planck function.
Parameters
----------
temperature : :class:`~astropy.units.Quantity`
Blackbody temperature.
scale : float or :class:`~astropy.units.Quantity`
Scale factor
Notes
-----
Model formula:
.. math:: B_{\\nu}(T) = A \\frac{2 h \\nu^{3} / c^{2}}{exp(h \\nu / k T) - 1}
Examples
--------
>>> from astropy.modeling import models
>>> from astropy import units as u
>>> bb = models.BlackBody(temperature=5000*u.K)
>>> bb(6000 * u.AA) # doctest: +FLOAT_CMP
<Quantity 1.53254685e-05 erg / (cm2 Hz s sr)>
.. plot::
:include-source:
import numpy as np
import matplotlib.pyplot as plt
from astropy.modeling.models import BlackBody
from astropy import units as u
from astropy.visualization import quantity_support
bb = BlackBody(temperature=5778*u.K)
wav = np.arange(1000, 110000) * u.AA
flux = bb(wav)
with quantity_support():
plt.figure()
plt.semilogx(wav, flux)
plt.axvline(bb.nu_max.to(u.AA, equivalencies=u.spectral()).value, ls='--')
plt.show()
"""
# We parametrize this model with a temperature and a scale.
temperature = Parameter(default=5000.0, min=0, unit=u.K)
scale = Parameter(default=1.0, min=0)
# We allow values without units to be passed when evaluating the model, and
# in this case the input x values are assumed to be frequencies in Hz.
_input_units_allow_dimensionless = True
# We enable the spectral equivalency by default for the spectral axis
input_units_equivalencies = {"x": u.spectral()}
def evaluate(self, x, temperature, scale):
"""Evaluate the model.
Parameters
----------
x : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Frequency at which to compute the blackbody. If no units are given,
this defaults to Hz.
temperature : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Temperature of the blackbody. If no units are given, this defaults
to Kelvin.
scale : float, `~numpy.ndarray`, or `~astropy.units.Quantity`
Desired scale for the blackbody.
Returns
-------
y : number or ndarray
Blackbody spectrum. The units are determined from the units of
``scale``.
.. note::
Use `numpy.errstate` to suppress Numpy warnings, if desired.
.. warning::
Output values might contain ``nan`` and ``inf``.
Raises
------
ValueError
Invalid temperature.
ZeroDivisionError
Wavelength is zero (when converting to frequency).
"""
if not isinstance(temperature, u.Quantity):
in_temp = u.Quantity(temperature, u.K)
else:
in_temp = temperature
# Convert to units for calculations, also force double precision
with u.add_enabled_equivalencies(u.spectral() + u.temperature()):
freq = u.Quantity(x, u.Hz, dtype=np.float64)
temp = u.Quantity(in_temp, u.K)
# check the units of scale and setup the output units
bb_unit = u.erg / (u.cm ** 2 * u.s * u.Hz * u.sr) # default unit
# use the scale that was used at initialization for determining the units to return
# to support returning the right units when fitting where units are stripped
if hasattr(self.scale, "unit") and self.scale.unit is not None:
# check that the units on scale are covertable to surface brightness units
if not self.scale.unit.is_equivalent(bb_unit, u.spectral_density(x)):
raise ValueError(
f"scale units not surface brightness: {self.scale.unit}"
)
# use the scale passed to get the value for scaling
if hasattr(scale, "unit"):
mult_scale = scale.value
else:
mult_scale = scale
bb_unit = self.scale.unit
else:
mult_scale = scale
# Check if input values are physically possible
if np.any(temp < 0):
raise ValueError(f"Temperature should be positive: {temp}")
if not np.all(np.isfinite(freq)) or np.any(freq <= 0):
warnings.warn(
"Input contains invalid wavelength/frequency value(s)",
AstropyUserWarning,
)
log_boltz = const.h * freq / (const.k_B * temp)
boltzm1 = np.expm1(log_boltz)
# Calculate blackbody flux
bb_nu = 2.0 * const.h * freq ** 3 / (const.c ** 2 * boltzm1) / u.sr
y = mult_scale * bb_nu.to(bb_unit, u.spectral_density(freq))
# If the temperature parameter has no unit, we should return a unitless
# value. This occurs for instance during fitting, since we drop the
# units temporarily.
if hasattr(temperature, "unit"):
return y
else:
return y.value
@property
def input_units(self):
# The input units are those of the 'x' value, which should always be
# Hz. Because we do this, and because input_units_allow_dimensionless
# is set to True, dimensionless values are assumed to be in Hz.
return {"x": u.Hz}
def _parameter_units_for_data_units(self, inputs_unit, outputs_unit):
return {"temperature": u.K}
@property
def bolometric_flux(self):
"""Bolometric flux."""
# bolometric flux in the native units of the planck function
native_bolflux = (
self.scale.value * const.sigma_sb * self.temperature ** 4 / np.pi
)
# return in more "astro" units
return native_bolflux.to(u.erg / (u.cm ** 2 * u.s))
@property
def lambda_max(self):
"""Peak wavelength when the curve is expressed as power density."""
return const.b_wien / self.temperature
@property
def nu_max(self):
"""Peak frequency when the curve is expressed as power density."""
return 2.8214391 * const.k_B * self.temperature / const.h
def ncrit(lamda_tables,
transition_upper,
transition_lower,
temperature,
OPR=3,
partners=['H2', 'OH2', 'PH2']):
"""
Compute the critical density for a transition given its temperature.
The critical density is defined as the Einstein A value divided by the sum
of the collision rates into the state minus the collision rates out of that
state. See Shirley et al 2015, eqn 4
(http://esoads.eso.org/cgi-bin/bib_query?arXiv:1501.01629)
Parameters
----------
lamda_tables : list
The list of LAMDA tables returned from a Lamda.query operation.
Should be [ collision_rates_dict, Avals/Freqs, Energy Levels ]
transition_upper : int
The upper transition number as indexed in the lamda catalog
transition_lower: int
The lower transition number as indexed in the lamda catalog
temperature : float
Kinetic temperature in Kelvin. Will be interpolated as appropriate.
Extrapolation uses nearest value
OPR : float
ortho/para ratio of h2 if para/ortho h2 are included as colliders
partners : list
A list of valid partners. It probably does not make sense to include
both electrons and H2 because they'll have different densities.
Returns
-------
ncrit : astropy.units.Quantity
A quantity with units cm^-3
"""
fortho = (OPR) / (OPR - 1)
# exclude partners that are explicitly excluded
crates = {
coll: val
for coll, val in lamda_tables[0].items() if coll in partners
}
avals = lamda_tables[1]
enlevs = lamda_tables[2]
aval = avals[(avals['Upper'] == transition_upper)
& (avals['Lower'] == transition_lower)]['EinsteinA'][0]
temperature_re = re.compile(r"C_ij\(T=([0-9]*)\)")
crate_temperatures = np.array([
int(temperature_re.search(cn).groups()[0])
for cn in crates[list(crates.keys())[0]].keys()
if temperature_re.search(cn)
])
if temperature < crate_temperatures.min():
crates_ji_all = {
coll: cr['C_ij(T={0})'.format(crate_temperatures.min())]
for coll, cr in crates.items()
}
elif temperature > crate_temperatures.max():
crates_ji_all = {
coll: cr['C_ij(T={0})'.format(crate_temperatures.max())]
for coll, cr in crates.items()
}
elif temperature in crate_temperatures:
crates_ji_all = {
coll: cr['C_ij(T={0})'.format(temperature)]
for coll, cr in crates.items()
}
else: # interpolate
nearest = np.argmin(np.abs(temperature - crate_temperatures))
if crate_temperatures[nearest] < temperature:
low, high = (crate_temperatures[nearest],
crate_temperatures[nearest + 1])
else:
low, high = (crate_temperatures[nearest - 1],
crate_temperatures[nearest])
crates_ji_all = {
coll:
(cr['C_ij(T={0})'.format(high)] - cr['C_ij(T={0})'.format(low)]) *
(temperature - low) / (high - low) + cr['C_ij(T={0})'.format(low)]
for coll, cr in crates.items()
}
transition_indices_ji = {
coll: np.nonzero(cr['Upper'] == transition_upper)[0]
for coll, cr in crates.items()
}
crates_ji = {
coll: crates_ji_all[coll][transition_indices_ji[coll]]
for coll in crates
}
# i > j: collisions from higher levels
transition_indices_ij = {
coll: np.nonzero(cr['Lower'] == transition_upper)[0]
for coll, cr in crates.items()
}
crates_ij = {}
for coll in crates.keys():
crates_ind = crates[coll][transition_indices_ij[coll]]
degeneracies_i = enlevs['Weight'][crates_ind['Upper'] - 1]
degeneracies_j = enlevs['Weight'][crates_ind['Lower'] - 1]
energy_i = enlevs['Energy'][crates_ind['Upper'] - 1] * u.cm**-1
energy_j = enlevs['Energy'][crates_ind['Lower'] - 1] * u.cm**-1
# Shirley 2015 eqn 4:
crates_ij[coll] = (crates_ji_all[coll][transition_indices_ij[coll]] *
degeneracies_i / degeneracies_j.astype('float') *
np.exp(
(-energy_i - energy_j).to(u.erg, u.spectral()) /
(constants.k_B * temperature * u.K)))
crates_tot_percollider = {
coll:
(np.sum(crates_ij[coll]) + np.sum(crates_ji[coll])) * u.cm**3 / u.s
for coll in crates
}
if 'OH2' in crates:
crates_tot = (fortho * crates_tot_percollider['OH2'] +
(1 - fortho) * crates_tot_percollider['PH2'])
elif 'PH2' in crates:
crates_tot = crates_tot_percollider['PH2']
elif 'H2' in crates:
crates_tot = crates_tot_percollider['H2']
return ((aval * u.s**-1) / crates_tot).to(u.cm**-3)
import astropy.units as u
# Can't find the vptable by default. So save it and feed it in manually
# vp.setpbimage(telescope='NOEMA')
# Create a Gaussian pb model b/c casa doesn't have a NOEMA/PdBI beam model?
fwhm = (((230.538 * u.GHz).to(u.m, u.spectral()) / (15 * u.m)) * u.rad).to(
u.deg).value
vp.setpbgauss(telescope='NOEMA',
dopb=True,
halfwidth=fwhm,
maxrad=4 * fwhm,
reffreq='230.538GHz')
vp.saveastable('noema_pb.tab')
tclean(
vis='meas_sets/M33-ARM05.ms',
datacolumn='data',
imagename="imaging/M33-ARM05_tclean_dirty",
field='M33*',
imsize=[1024, 700],
cell='0.2arcsec',
specmode='cube',
start=1,
width=1,
nchan=-1,
startmodel=None,
gridder='mosaic',
weighting='natural',
niter=0,
def _get_url_for_timerange(self, timerange, **kwargs):
"""
Returns urls to the SUVI data for the specified time range.
Parameters
----------
timerange: `sunpy.time.TimeRange`
Time range for which data is to be downloaded.
level : `str`, optional
The level of the data. Possible values are 1b and 2 (default).
wavelength : `astropy.units.Quantity` or `tuple`, optional
Wavelength band. If not given, all wavelengths are returned.
satellitenumber : `int`, optional
GOES satellite number. Must be >= 16. Default is 16.
"""
base_url = "https://data.ngdc.noaa.gov/platforms/solar-space-observing-satellites/goes/goes{goes_number}/"
supported_waves = [94, 131, 171, 195, 284, 304]
supported_levels = ("2", "1b")
# these are optional requirements so if not provided assume defaults
# if wavelength is not provided assuming all of them
if "wavelength" in kwargs.keys():
wavelength_input = kwargs.get("wavelength")
if isinstance(wavelength_input, u.Quantity): # not a range
if int(wavelength_input.to_value('Angstrom')) not in supported_waves:
raise ValueError(f"Wavelength {kwargs.get('wavelength')} not supported.")
else:
wavelength = [kwargs.get("wavelength")]
else: # Range was provided
compress_index = [wavelength_input.wavemin <= this_wave <=
wavelength_input.wavemax for this_wave in (supported_waves * u.Angstrom)]
if not any(compress_index):
raise ValueError(
f"Wavelength {wavelength_input} not supported.")
else:
wavelength = list(compress(supported_waves, compress_index)) * u.Angstrom
else: # no wavelength provided return all of them
wavelength = supported_waves * u.Angstrom
# check that the input wavelength can be converted to angstrom
waves = [int(this_wave.to_value('angstrom', equivalencies=u.spectral()))
for this_wave in wavelength]
# use the given satellite number or choose the best one
satellitenumber = int(kwargs.get(
"satellitenumber", self._get_goes_sat_num(timerange.start)))
if satellitenumber < 16:
raise ValueError(f"Satellite number {satellitenumber} not supported.")
# default to the highest level of data
level = str(kwargs.get("level", "2")) # make string in case the input is a number
if level not in supported_levels:
raise ValueError(f"Level {level} is not supported.")
results = []
for this_wave in waves:
if level == "2":
search_pattern = base_url + \
'l{level}/data/suvi-l{level}-ci{wave:03}/%Y/%m/%d/dr_suvi-l{level}-ci{wave:03}_g{goes_number}_s%Y%m%dT%H%M%SZ_.*\.fits'
elif level == "1b":
if this_wave in [131, 171, 195, 284]:
search_pattern = base_url + \
'l{level}/suvi-l{level}-fe{wave:03}/%Y/%m/%d/OR_SUVI-L{level}-Fe{wave:03}_G{goes_number}_s%Y%j%H%M%S.*\.fits.gz'
elif this_wave == 304:
search_pattern = base_url + \
'l{level}/suvi-l{level}-he{wave:03}/%Y/%m/%d/OR_SUVI-L{level}-He{wave_minus1:03}_G{goes_number}_s%Y%j%H%M%S.*\.fits.gz'
elif this_wave == 94:
search_pattern = base_url + \
'l{level}/suvi-l{level}-fe{wave:03}/%Y/%m/%d/OR_SUVI-L{level}-Fe{wave_minus1:03}_G{goes_number}_s%Y%j%H%M%S.*\.fits.gz'
if search_pattern.count('wave_minus1'):
scraper = Scraper(search_pattern, level=level, wave=this_wave,
goes_number=satellitenumber, wave_minus1=this_wave-1)
else:
scraper = Scraper(search_pattern, level=level, wave=this_wave,
goes_number=satellitenumber)
results.extend(scraper.filelist(timerange))
return results
def write_fits_image(dataset,
image,
image_parameters,
filename,
channel,
beam=None,
bunit='Jy/beam',
extra_fits_headers=None):
"""Write an image to a FITS file.
Parameters
----------
dataset : :class:`katsdpimager.loader_core.LoaderBase`
Source dataset (used to set metadata such as phase centre)
image : :class:`numpy.ndarray`
Image data in Jy/beam, indexed by polarization, m, l. For
a 2M x 2N image, the phase centre is at coordinates (M, N).
image_parameters : :class:`katsdpimager.parameters.ImageParameters`
Metadata associated with the image
filename : str
File to write. It is silently overwritten if already present.
channel : int
Channel number to substitute into `filename` with printf formatting.
beam : :class:`katsdpimager.beam.Beam`, optional
Synthesized beam model to write to the header
bunit : str, optional
Value for the ``BUNIT`` header in the file. It can be explicitly set
to ``None`` to avoid writing this key.
extra_fits_headers : mapping, optional
Extra headers to add to the FITS headers present.
Returns
-------
image
Image data that is written to the file (in the order expected by
:mod:`astropy.io.fits`).
header
FITS headers.
Raises
------
ValueError
If the set of `polarizations` cannot be represented as a linear
transform in the FITS header.
"""
header = fits.Header()
if bunit is not None:
header['BUNIT'] = bunit
header['ORIGIN'] = 'katsdpimager'
header['HISTORY'] = f'Created by katsdpimager {katsdpimager.__version__}'
header['TIMESYS'] = 'UTC'
header['DATE'] = Time.now().utc.isot
# Transformation from pixel coordinates to intermediate world coordinates,
# which are taken to be l, m coordinates. The reference point is currently
# taken to be the centre of the image (actually half a pixel beyond the
# centre, because of the way fftshift works). Note that astropy.io.fits
# reverses the axis order. The X coordinate is computed differently
# because the X axis is flipped to allow RA to increase right-to-left.
header['CRPIX1'] = image.shape[2] * 0.5
header['CRPIX2'] = image.shape[1] * 0.5 + 1.0
header['CRPIX4'] = 1.0
# FITS uses degrees; and RA increases right-to-left
delt = np.arcsin(image_parameters.pixel_size).to(units.deg).value
header['CDELT1'] = -delt
header['CDELT2'] = delt
header['CDELT4'] = 1.0
# Transformation from intermediate world coordinates to world
# coordinates (celestial coordinates in this case).
# TODO: get equinox from input
phase_centre = dataset.phase_centre()
header['EQUINOX'] = 2000.0
header['RADESYS'] = 'FK5' # Julian equinox
header['CUNIT1'] = 'deg'
header['CUNIT2'] = 'deg'
header['CUNIT4'] = 'Hz'
header['CTYPE1'] = 'RA---SIN'
header['CTYPE2'] = 'DEC--SIN'
header['CTYPE4'] = 'FREQ '
header['CRVAL1'] = phase_centre[0].to(units.deg).value
header['CRVAL2'] = phase_centre[1].to(units.deg).value
header['CRVAL4'] = image_parameters.wavelength.to(
units.Hz, equivalencies=units.spectral()).value
if beam is not None:
major = beam.major * image_parameters.pixel_size * units.rad
minor = beam.minor * image_parameters.pixel_size * units.rad
header['BMAJ'] = major.to(units.deg).value
header['BMIN'] = minor.to(units.deg).value
header['BPA'] = beam.theta.to(units.deg).value
_fits_polarizations(header, 3, image_parameters.fixed.polarizations)
# This is basically np.nanmin and np.nanmax, but the implementations of
# those take a slow, safe path if the array is a subclass of ndarray. In
# our case it is but the fast path still works so we use it directly.
datamin = float(np.fmin.reduce(image, axis=None))
datamax = float(np.fmax.reduce(image, axis=None))
if not np.isnan(datamin):
header['DATAMIN'] = datamin
header['DATAMAX'] = datamax
header.update(dataset.extra_fits_headers())
if extra_fits_headers is not None:
header.update(extra_fits_headers)
# l axis is reversed, because RA increases right-to-left.
# The np.newaxis adds an axis for frequency. While it's not required for
# the FITS file to be valid (it's legal for the WCS transformations to
# reference additional virtual axes), aplpy 1.1.1 doesn't handle it
# (https://github.com/aplpy/aplpy/issues/350).
image = image[np.newaxis, :, :, ::-1]
# Explicitly converting to big-endian has two advantages:
# 1. It returns a contiguous array, which allows for a much faster path
# through writeto.
# 2. If the image is little-endian, then astropy.io.fits will convert to
# big endian, write, and convert back again.
# The disadvantage is an increase in memory usage.
#
image_be = np.require(image, image.dtype.newbyteorder('>'), 'C')
hdu = fits.PrimaryHDU(image_be, header)
hdu.writeto(filename, overwrite=True)
return image, header
class Conf():
# acceptable field names for DataClass
fieldnames_info = [
# General
{
'description': 'Target Identifier',
'fieldnames': ['targetname', 'id', 'Object'],
'provenance': ['orbit', 'ephem', 'obs', 'phys'],
'dimension': None
},
{
'description': 'Target Designation',
'fieldnames': ['desig', 'designation'],
'provenance': ['orbit', 'ephem', 'obs', 'phys'],
'dimension': None
},
{
'description': 'Target Number',
'fieldnames': ['number'],
'provenance': ['orbit', 'ephem', 'obs', 'phys'],
'dimension': None
},
{
'description': 'Target Name',
'fieldnames': ['name'],
'provenance': ['orbit', 'ephem', 'obs', 'phys'],
'dimension': None
},
{
'description': 'Epoch',
'fieldnames':
['epoch', 'datetime', 'Date', 'date', 'Time', 'time'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.time_object
},
# Orbital Elements
{
'description': 'Semi-Major Axis',
'fieldnames': ['a', 'sma'],
'provenance': ['orbit'],
'dimension': dimensions.length
},
{
'description': 'Eccentricity',
'fieldnames': ['e', 'ecc'],
'provenance': ['orbit'],
'dimension': dimensions.dimensionless
},
{
'description': 'Inclination',
'fieldnames': ['i', 'inc', 'incl'],
'provenance': ['orbit'],
'dimension': dimensions.angle
},
{
'description': 'Perihelion Distance',
'fieldnames': ['q', 'periheldist'],
'provenance': ['orbit'],
'dimension': dimensions.length
},
{
'description': 'Aphelion Distance',
'fieldnames': ['Q', 'apheldist'],
'provenance': ['orbit'],
'dimension': dimensions.length
},
{
'description': 'Longitude of the Ascending Node',
'fieldnames': ['Omega', 'longnode', 'node'],
'provenance': ['orbit'],
'dimension': dimensions.angle
},
{
'description': 'Argument of the Periapsis',
'fieldnames': ['w', 'argper'],
'provenance': ['orbit'],
'dimension': dimensions.angle
},
{
'description': 'Mean Anomaly',
'fieldnames': ['M', 'mean_anom'],
'provenance': ['orbit'],
'dimension': dimensions.angle
},
{
'description': 'True Anomaly',
'fieldnames': ['v', 'true_anom', 'true_anomaly'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Arc Length',
'fieldnames': ['arc', 'arc_length'],
'provenance': ['orbit', 'ephem'],
'dimension': dimensions.time
},
{
'description': 'Delta-v',
'fieldnames': ['delta_v', 'delta-v'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length_per_time
},
{
'description': 'Minimum Orbit Intersection Distance wrt Mercury',
'fieldnames': ['moid_mercury'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Earth',
'fieldnames': ['moid_earth'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Venus',
'fieldnames': ['moid_venus'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Mars',
'fieldnames': ['moid_mars'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Jupiter',
'fieldnames': ['moid_jupiter'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Saturn',
'fieldnames': ['moid_saturn'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Uranus',
'fieldnames': ['moid_uranus'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Minimum Orbit Intersection Distance wrt Neptune',
'fieldnames': ['moid_neptune'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.length
},
{
'description': 'Tisserand Parameter wrt Jupiter',
'fieldnames': ['Tj', 'tj'],
'provenance': ['orbit', 'phys'],
'dimension': None
},
{
'description': 'MPC Orbit Type',
'fieldnames': ['mpc_orb_type'],
'provenance': ['orbit', 'phys'],
'dimension': None
},
{
'description': 'Epoch of Perihelion Passage',
'fieldnames': ['Tp'],
'provenance': ['orbit'],
'dimension': dimensions.time_object
},
{
'description': 'Orbital Period',
'fieldnames': ['P', 'period'],
'provenance': ['orbit', 'phys'],
'dimension': dimensions.time
},
# Ephemerides properties
{
'description': 'Heliocentric Distance',
'fieldnames': ['r', 'rh', 'r_hel', 'heldist'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Heliocentric Radial Velocity',
'fieldnames':
['r_rate', 'rh_rate', 'rdot', 'r-dot', 'rhdot', 'rh-dot'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'Distance to the Observer',
'fieldnames': ['delta', 'Delta', 'obsdist'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length
},
{
'description':
'Observer-Target Radial Velocity',
'fieldnames':
['delta_rate', 'deltadot', 'delta-dot', 'deldot', 'del-dot'],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.length_per_time
},
{
'description': 'Right Ascension',
'fieldnames': ['ra', 'RA'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Declination',
'fieldnames': ['dec', 'DEC', 'Dec'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description':
'Right Ascension Rate',
'fieldnames':
['ra_rate', 'RA_rate', 'ra_rates', 'RA_rates', 'dRA', 'dra'],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.angle_per_time
},
{
'description':
'RA*cos(Dec) Rate',
'fieldnames': [
'RA*cos(Dec)_rate', 'dra cos(dec)', 'dRA cos(Dec)',
'dra*cos(dec)', 'dRA*cos(Dec)'
],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.angle_per_time
},
{
'description':
'Declination Rate',
'fieldnames': [
'dec_rate', 'DEC_rate', 'Dec_rate', 'dec_rates', 'DEC_rates',
'Dec_rates', 'dDec', 'dDEC', 'ddec'
],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.angle_per_time
},
{
'description': 'Proper Motion',
'fieldnames': ['mu', 'Proper motion'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle_per_time
},
{
'description': 'Proper Motion Direction',
'fieldnames': ['Direction', 'direction'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Solar Phase Angle',
'fieldnames': ['alpha', 'phaseangle', 'Phase', 'phase'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description':
'Solar Elongation Angle',
'fieldnames': [
'elong', 'solarelong', 'solarelongation', 'elongation',
'Elongation'
],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.angle
},
{
'description': 'V-band Magnitude',
'fieldnames': ['V', 'Vmag'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude
},
{
'description': 'Heliocentric Ecliptic Longitude',
'fieldnames':
['hlon', 'EclLon', 'ecllon', 'HelEclLon', 'helecllon'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Heliocentric Ecliptic Latitude',
'fieldnames':
['hlat', 'EclLat', 'ecllat', 'HelEclLat', 'helecllat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Horizontal Elevation',
'fieldnames':
['el', 'EL', 'elevation', 'alt', 'altitude', 'Altitude'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Horizontal Azimuth',
'fieldnames': ['az', 'AZ', 'azimuth'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description':
'Lunar Elongation',
'fieldnames': [
'lunar_elong', 'elong_moon', 'elongation_moon',
'lunar_elongation', 'lunarelong'
],
'provenance': ['ephem', 'obs'],
'dimension':
dimensions.angle
},
{
'description': 'X State Vector Component',
'fieldnames': ['x', 'X', 'x_vec'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Y State Vector Component',
'fieldnames': ['y', 'Y', 'y_vec'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Z State Vector Component',
'fieldnames': ['z', 'Z', 'z_vec'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'X Velocity Vector Component',
'fieldnames': ['vx', 'dx', 'dx/dt'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'Y Velocity Vector Component',
'fieldnames': ['vy', 'dy', 'dy/dt'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'Z Velocity Vector Component',
'fieldnames': ['vz', 'dz', 'dz/dt'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'X heliocentric position vector',
'fieldnames': ['x_h', 'X_h'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Y heliocentric position vector',
'fieldnames': ['y_h', 'Y_h'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Z heliocentric position vector',
'fieldnames': ['z_h', 'Z_h'],
'provenance': ['orbit', 'ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': 'Comet Total Absolute Magnitude',
'fieldnames': ['m1', 'M1'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude
},
{
'description': 'Comet Nuclear Absolute Magnitude',
'fieldnames': ['m2', 'M2'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude
},
{
'description': 'Total Magnitude Scaling Factor',
'fieldnames': ['k1', 'K1'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.dimensionless
},
{
'description': 'Nuclear Magnitude Scaling Factor',
'fieldnames': ['k2', 'K2'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.dimensionless
},
{
'description': 'Phase Coefficient',
'fieldnames': ['phase_coeff', 'Phase_coeff'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.dimensionless
},
{
'description': 'Information on Solar Presence',
'fieldnames': ['solar_presence', 'Solar_presence'],
'provenance': ['ephem', 'obs'],
'dimension': None
},
{
'description': 'Information on Moon and target status',
'fieldnames': ['status_flag', 'Status_flag'],
'provenance': ['ephem', 'obs'],
'dimension': None
},
{
'description': 'Apparent Right Ascension',
'fieldnames': ['RA_app', 'ra_app'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Apparent Declination',
'fieldnames': ['DEC_app', 'dec_app'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Azimuth Rate (dAZ*cosE)',
'fieldnames': ['az_rate', 'AZ_rate'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle_per_time
},
{
'description': 'Elevation Rate (d(ELV)/dt)',
'fieldnames': ['el_rate', 'EL_rate'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle_per_time
},
{
'description': 'Satellite Position Angle',
'fieldnames': ['sat_pang', 'Sat_pang'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Local Sidereal Time',
'fieldnames': ['siderealtime', 'Siderealtime'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': 'Target Optical Airmass',
'fieldnames': ['airmass', 'Airmass'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.dimensionless
},
{
'description': 'V Magnitude Extinction',
'fieldnames': ['vmagex', 'Vmagex'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude
},
{
'description': 'Surface Brightness',
'fieldnames': ['Surfbright', 'surfbright'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude_per_solid_angle
},
{
'description': 'Fraction of Illumination',
'fieldnames': ['frac_illum', 'Frac_illum'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.percent
},
{
'description': 'Illumination Defect',
'fieldnames': ['defect_illum', 'Defect_illum'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target-primary angular separation',
'fieldnames': ['targ_sep', 'Targ_sep'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target-primary visibility',
'fieldnames': ['targ_vis', 'Targ_vis'],
'provenance': ['ephem', 'obs'],
'dimension': None
},
{
'description': 'Angular width of target',
'fieldnames': ['targ_width', 'Targ_width'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Apparent planetodetic longitude',
'fieldnames': ['pldetic_long', 'Pldetic_long'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Apparent planetodetic latitude',
'fieldnames': ['pldetic_lat', 'Pldetic_lat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Apparent planetodetic Solar longitude',
'fieldnames': ['pltdeticSol_long', 'PltdeticSol_long'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Apparent planetodetic Solar latitude',
'fieldnames': ['pltdeticSol_lat', 'PltdeticSol_lat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target sub-solar point position angle',
'fieldnames': ['subsol_ang', 'Subsol_ang'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target sub-solar point angle distance',
'fieldnames': ['subsol_dist', 'Subsol_dist'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target North pole position angle',
'fieldnames': ['npole_angle', 'Npole_angle'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target North pole position distance',
'fieldnames': ['npole_dist', 'Npole_dist'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Observation centric ecliptic longitude',
'fieldnames': ['obs_ecl_long', 'Obs_ecl_long'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Observation centric ecliptic latitude',
'fieldnames': ['obs_ecl_lat', 'Obs_ecl_lat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'One-way light time',
'fieldnames': ['lighttime', 'Lighttime'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': 'Target center velocity wrt Sun',
'fieldnames': ['vel_sun', 'Vel_sun'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'Target center velocity wrt Observer',
'fieldnames': ['vel_obs', 'Vel_obs'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': 'Lunar illumination',
'fieldnames': ['lun_illum', 'Lun_illum'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.percent
},
{
'description': 'Apparent interfering body elongation wrt observer',
'fieldnames': ['ib_elong', 'IB_elong'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Interfering body illumination',
'fieldnames': ['ib_illum', 'IB_illum'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.percent
},
{
'description': 'Observer primary target angle',
'fieldnames': ['targ_angle_obs', 'Targ_angle_obs'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Orbital plane angle',
'fieldnames': ['orbangle_plane', 'Orbangle_plane'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Constellation ID containing target',
'fieldnames': ['constellation', 'Constellation'],
'provenance': ['ephem', 'obs'],
'dimension': None
},
{
'description': 'Target North Pole RA',
'fieldnames': ['targ_npole_ra', 'targ_npole_RA'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Target North Pole DEC',
'fieldnames': ['targ_npole_dec', 'targ_npole_DEC'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Galactic Longitude',
'fieldnames': ['glx_long', 'Glx_long'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Galactic Latitude',
'fieldnames': ['glx_lat', 'Glx_lat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Local apparent solar time',
'fieldnames': ['solartime'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': 'Observer light time from Earth',
'fieldnames': ['earthlighttime', 'Earthlighttime'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': '3 sigma positional uncertainty RA',
'fieldnames': ['RA_3sigma', 'ra_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma positional uncertainty DEC',
'fieldnames': ['DEC_3sigma', 'dec_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma positional uncertainty semi-major axis',
'fieldnames': ['sma_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma positional uncertainty semi-minor axis',
'fieldnames': ['smi_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma positional uncertainty position angle',
'fieldnames': ['posangle_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma positional uncertainty ellipse area',
'fieldnames': ['area_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.solid_angle
},
{
'description': '3 sigma positional uncertainty root sum square',
'fieldnames': ['rss_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': '3 sigma range uncertainty',
'fieldnames': ['r_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length
},
{
'description': '3 sigma range rate uncertainty',
'fieldnames': ['r_rate_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.length_per_time
},
{
'description': '3 sigma doppler radar uncertainty at S-band',
'fieldnames': ['sband_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.frequency
},
{
'description': '3 sigma doppler radar uncertainty at X-band',
'fieldnames': ['xband_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.frequency
},
{
'description': '3 sigma doppler round-trip delay uncertainty',
'fieldnames': ['dopdelay_3sigma'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': 'Local apparent hour angle',
'fieldnames': ['locapp_hourangle'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.time
},
{
'description': 'True phase angle',
'fieldnames': ['true_phaseangle'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Phase angle bisector longitude',
'fieldnames': ['pab_long'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Phase angle bisector latitude',
'fieldnames': ['pab_lat'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Absolute V-band Magnitude',
'fieldnames': ['abs_V', 'abs_Vmag'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.magnitude
},
{
'description': 'Satellite X-position',
'fieldnames': ['sat_X', 'sat_x'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Satellite Y-position',
'fieldnames': ['sat_y', 'sat_Y'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
{
'description': 'Atmospheric Refraction',
'fieldnames': ['atm_refraction', 'refraction'],
'provenance': ['ephem', 'obs'],
'dimension': dimensions.angle
},
# Physical properties (dependent on other properties)
{
'description': 'Infrared Beaming Parameter',
'fieldnames': ['eta', 'Eta'],
'provenance': ['ephem', 'obs'],
'dimension': None
},
{
'description': 'Temperature',
'fieldnames': ['temp', 'Temp', 'temperature', 'Temperature'],
'provenance': ['phys', 'ephem', 'obs'],
'dimension': dimensions.temperature
},
# Physical properties (static)
{
'description': 'Effective Diameter',
'fieldnames': ['d', 'D', 'diam', 'diameter', 'Diameter'],
'provenance': ['phys'],
'dimension': dimensions.length
},
{
'description': 'Effective Radius',
'fieldnames': ['R', 'radius'],
'provenance': ['phys'],
'dimension': dimensions.length
},
{
'description': 'Geometric Albedo',
'fieldnames': ['pv', 'pV', 'p_v', 'p_V', 'geomalb'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Bond Albedo',
'fieldnames': ['A', 'bondalbedo'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Emissivity',
'fieldnames': ['emissivity', 'Emissivity'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Absolute Magnitude',
'fieldnames': ['absmag', 'H'],
'provenance': ['phys', 'ephem', 'orbit'],
'dimension': dimensions.magnitude
},
{
'description': 'Photometric Phase Slope Parameter',
'fieldnames': ['G', 'slope'],
'provenance': ['phys', 'ephem', 'orbit'],
'dimension': dimensions.dimensionless
},
{
'description': 'Molecule Identifier',
'fieldnames': ['mol_tag', 'mol_name'],
'provenance': ['phys'],
'dimension': None
},
{
'description': 'Transition frequency',
'fieldnames': ['t_freq'],
'provenance': ['phys'],
'dimension': dimensions.frequency,
'equivalencies': u.spectral()
},
{
'description': 'Integrated line intensity at 300 K',
'fieldnames': ['lgint300'],
'provenance': ['phys'],
'dimension': None
}, # fix when intensity units are resolved
{
'description':
'Integrated line intensity at designated Temperature',
'fieldnames': ['intl', 'lgint'],
'provenance': ['phys'],
'dimension': None
}, # fix when intensity units are resolved
{
'description': 'Partition function at 300 K',
'fieldnames': ['partfn300'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Partition function at designated temperature',
'fieldnames': ['partfn'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Upper state degeneracy',
'fieldnames': ['dgup'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Upper level energy in Joules',
'fieldnames': ['eup_j', 'eup_J'],
'provenance': ['phys'],
'dimension': dimensions.energy
},
{
'description': 'Lower level energy in Joules',
'fieldnames': ['elo_j', 'elo_J'],
'provenance': ['phys'],
'dimension': dimensions.energy
},
{
'description': 'Degrees of freedom',
'fieldnames': ['degfr', 'ndf', 'degfreedom'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Einstein Coefficient',
'fieldnames': ['au', 'eincoeff'],
'provenance': ['phys'],
'dimension': dimensions.inverse_time
},
{
'description': 'Timescale * r^2',
'fieldnames': ['beta', 'beta_factor'],
'provenance': ['phys'],
'dimension': dimensions.time_area
},
{
'description': 'Total Number',
'fieldnames': ['totnum', 'total_number_nocd'
'total_number'],
'provenance': ['phys'],
'dimension': dimensions.dimensionless
},
{
'description': 'Column Density from Bockelee Morvan et al. 2004',
'fieldnames': ['cdensity', 'col_density'],
'provenance': ['phys'],
'dimension': dimensions.inverse_area
},
# { # see module doc string
# 'description': '',
# 'fieldnames': [],
# 'provenance': [],
# 'dimension': None,
# 'equivalencies': (astropy units equivalencies, e.g., u.spectral())
# },
]
# use this code snippet to identify duplicate field names:
# from sbpy.data import Conf
# import collections
# a = sum(Conf.fieldnames, [])
# print([item for item, count in collections.Counter(a).items()
# if count > 1])
# list of fieldnames; each element a list of alternatives
fieldnames = [prop['fieldnames'] for prop in fieldnames_info]
fieldname_idx = {}
for idx, field in enumerate(fieldnames):
for alt in field:
fieldname_idx[alt] = idx
# field equivalencies defining conversions
# key defines target quantity; dict with source quantity and function
# for conversion
# conversions considered as part of DataClass._translate_columns
field_eq = {
'R': {
'd': lambda r: r / 2
},
# diameter to radius}
'd': {
'R': lambda d: d * 2
}
}
# definitions for use of pyoorb in Orbits
oorb_timeScales = {'UTC': 1, 'UT1': 2, 'TT': 3, 'TAI': 4}
oorb_elemType = {'CART': 1, 'COM': 2, 'KEP': 3, 'DEL': 4, 'EQX': 5}
# field name, unit; in order as returned from oorb
# However, in propagate, angular units are returned as deg. This is
# accounted for in Orbit.oo_propagate().
oorb_orbit_fields = {
'COM': (
('id', None),
('q', 'au'),
('e', ''),
('incl', 'rad'),
('Omega', 'rad'),
('w', 'rad'),
('Tp', 'd'),
('orbtype', None),
('epoch', 'd'),
('epoch_scale', None),
('H', 'mag'),
('G', ''),
),
'KEP': (
('id', None),
('a', 'au'),
('e', ''),
('incl', 'rad'),
('Omega', 'rad'),
('w', 'rad'),
('M', 'rad'),
('orbtype', None),
('epoch', 'd'),
('epoch_scale', None),
('H', 'mag'),
('G', ''),
),
'CART': (
('id', None),
('x', 'au'),
('y', 'au'),
('z', 'au'),
('vx', 'au/d'),
('vy', 'au/d'),
('vz', 'au/d'),
('orbtype', None),
('epoch', 'd'),
('epoch_scale', None),
('H', 'mag'),
('G', ''),
)
}
oorb_ephem_full_fields = [
'MJD', 'RA', 'DEC', 'RA*cos(Dec)_rate', 'DEC_rate', 'alpha', 'elong',
'r', 'Delta', 'V', 'pa', 'TopEclLon', 'TopEclLat', 'OppTopEclLon',
'OppTopEclLat', 'HelEclLon', 'HelEclLat', 'OppHelEclLon',
'OppHelEclLat', 'EL', 'ELsun', 'ELmoon', 'lunarphase', 'lunarelong',
'x', 'y', 'z', 'vx', 'vy', 'vz', 'obsx', 'obsy', 'obsz', 'trueanom'
]
oorb_ephem_full_units = [
'd', 'deg', 'deg', 'deg/d', 'deg/d', 'deg', 'deg', 'au', 'au', 'mag',
'deg', 'deg', 'deg', 'deg', 'deg', 'deg', 'deg', 'deg', 'deg', 'deg',
'deg', 'deg', None, 'deg', 'au', 'au', 'au', 'au/d', 'au/d', 'au/d',
'au', 'au', 'au', 'deg'
]
oorb_ephem_basic_fields = [
'MJD', 'RA', 'DEC', 'RA*cos(Dec)_rate', 'DEC_rate', 'alpha', 'elong',
'r', 'Delta', 'V', 'trueanom'
]
oorb_ephem_basic_units = [
'd', 'deg', 'deg', 'deg/d', 'deg/d', 'deg', 'deg', 'au', 'au', 'mag',
'deg'
]
# definitions for MPC orbits: MPC field name: [sbpy field name, unit]
mpc_orbit_fields = {
'absolute_magnitude': ['absmag', 'mag'],
'aphelion_distance': ['Q', 'au'],
'arc_length': ['arc', 'day'],
'argument_of_perihelion': ['w', 'deg'],
'ascending_node': ['Omega', 'deg'],
'delta_v': ['delta_v', 'km/s'],
'designation': ['desig', None],
'earth_moid': ['moid_earth', 'au'],
'eccentricity': ['e', ''],
'epoch_jd': ['epoch', 'time_jd_utc'],
'inclination': ['i', 'deg'],
'jupiter_moid': ['moid_jupiter', 'au'],
'mars_moid': ['moid_mars', 'au'],
'mean_anomaly': ['M', 'deg'],
'mercury_moid': ['moid_mercury', 'au'],
'name': ['name', None],
'number': ['number', None],
'orbit_type': ['mpc_orbit_type', None],
'perihelion_date_jd': ['Tp', 'time_jd_utc'],
'perihelion_distance': ['q', 'au'],
'period': ['P', 'year'],
'phase_slope': ['G', ''],
'saturn_moid': ['moid_saturn', 'au'],
'semimajor_axis': ['a', 'au'],
'tisserand_jupiter': ['Tj', ''],
'uranus_moid': ['moid_uranus', 'au'],
'venus_moid': ['moid_venus', 'au']
}
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import os, imp
import warnings as warn
import pdb
from scipy.integrate import simps
from scipy.interpolate import interp1d
from astropy import units as u
from astropy import constants as const
# Path
pyigm_path = imp.find_module('pyigm')[1]
Ryd = const.Ryd.to('eV', equivalencies=u.spectral())
class CUBA(object):
"""
Class for CUBA analysis
JXP on 13 Oct 2015
Attributes
----------
fits_path : str, optional
Path to the FITS data files for COS-Halos
z : ndarray
Array of z values from CUBA file
energy : Quantity array
def test_wave_conversion(in_q, out_u, ans):
"""Full equivalencies test with direct conversion."""
result = in_q.to(out_u, equivalencies=u.spectral())
np.testing.assert_allclose(result.value, ans.value)
assert result.unit == ans.unit
def ghz_to_um(ghz_value):
lam = (ghz_value * u.GHz).to(u.um, equivalencies=u.spectral())
return lam.value
def __init__(self,fn,x_min=1e-10,x_max=1e10,unit='micron',\
min_strength=None,max_exc=None):
'''
Creating a LineList object.
@param fn: The full path and filename to the spectroscopy file. Must
contain either the CDMS or the JPL string.
@type fn: str
@keyword x_min: Minimum value for reading data in frequency/wavelength
If default, the lowest frequency is the one in the file.
(default: 1e-10)
@type x_min: float
@keyword x_max: Maximum value for reading data in frequency/wavelength
If default, the highest frequency is the one in the file
(default: 1e10)
@type x_max: float
@keyword unit: Unit of x_min/x_max (micron,GHz,MHz,Hz). Any
astropy.constants unit works. This can also be a Unit()
class object.
(default: 'micron')
@type unit: string
@keyword min_strength: if None all are included, else only lines with
strengths above this value are included
(log scale, nm2*Mhz)
(default: None)
@type min_strength: float
@keyword max_exc: if None all are included, else only lines with
excitation energies below this value are included
(cm-1)
(default: None)
@type max_exc: float
'''
self.fn = fn
self.min_strength = min_strength
self.max_exc = max_exc
#-- Figure out if it's a JPL or a CDMS catalog
if self.fn.upper().find('JPL') != -1:
self.catstring = 'JPL'
else:
self.catstring = 'CDMS'
#-- Grab the unit
if isinstance(unit,
str) and unit.lower() in ['1 / cm', 'cm-1', 'cm^-1']:
unit = u.Unit("1 / cm")
elif isinstance(unit, str):
unit = getattr(u, unit)
#-- Convert the units to the default MHz (unit of the files), but
# reverse min/max in case a wavelength is given. Wave number/Frequency
# are OK
if unit.is_equivalent(u.micron):
self.x_min = (x_max * unit).to(u.MHz, equivalencies=u.spectral())
self.x_max = (x_min * unit).to(u.MHz, equivalencies=u.spectral())
else:
self.x_max = (x_max * unit).to(u.MHz, equivalencies=u.spectral())
self.x_min = (x_min * unit).to(u.MHz, equivalencies=u.spectral())
#-- Initialise the internal line list and read.
self.line_list = []
self.read()
def um_to_ghz(um_value):
freq = (um_value * u.um).to(u.GHz, equivalencies=u.spectral())
return freq.value
def energy(self):
"""
The energy of the spectral axis as a `~astropy.units.Quantity` in units
of eV.
"""
return self.spectral_axis.to(u.eV, u.spectral())
58
! NUMBER OF ENERGY LEVELS
{nlev}
!LEVEL + ENERGIES(cm^-1) + WEIGHT + J + V
""".format(nlev=(maxv + 1) * (maxj + 1)))
ii = 1
leveldict = {}
levelenergy = {}
for vv in range(0, maxv + 1):
if ii in leveldict.values():
raise ValueError((vv, ))
leveldict[(vv, 0)] = ii #1 + maxj*vv
energy_K = groundstates[(vv, 0)]
energy = (energy_K * u.K).to(u.eV, u.temperature_energy()).to(
u.cm**-1, u.spectral()).value
levelenergy[(vv, 0)] = energy
degen = 16
# manually write out the ground state, since it's not in the table
fh.write("{0:5d} {1:15.9f} {2:5.1f} {4:5d}_{3:d}\n".format(
ii, energy, degen, 0, vv))
ii += 1
for jj in range(1, maxj + 1):
row = NaCl[(NaCl['vu'] == vv) & (NaCl['Ju'] == jj)]
energy = row['E_U'].quantity[0].to(
u.eV, u.temperature_energy()).to(u.cm**-1, u.spectral()).value
degen = 16 + 32 * jj
fh.write("{0:5d} {1:15.9f} {2:5.1f} {4:5d}_{3:d}\n".format(
ii, energy, degen, jj, vv))
if ii in leveldict.values():
raise ValueError((vv, jj))
def frequency(self):
"""
The `spectral_axis` as a `~astropy.units.Quantity` in units of GHz
"""
return self.spectral_axis.to(u.GHz, u.spectral())
def from_jplspec(cls, temp_estimate, transition_freq, mol_tag):
"""Returns relevant constants from JPLSpec catalog and energy
calculations
Parameters
----------
temp_estimate : `~astropy.units.Quantity`
Estimated temperature in Kelvins
transition_freq : `~astropy.units.Quantity`
Transition frequency in MHz
mol_tag : int or str
Molecule identifier. Make sure it is an exclusive identifier,
although this function can take a regex as your molecule tag,
it will return an error if there is ambiguity on what the
molecule of interest is. The function
`~astroquery.jplspec.JPLSpec.query_lines_async`
with the option `parse_name_locally=True` can be used to parse
for the exclusive identifier of a molecule you might be
interested in. For more information, visit
`astroquery.jplspec` documentation.
Returns
-------
data : `~sbpy.data.Phys`
Quantities in the following order from JPL Spectral Molecular
Catalog:
* Transition frequency
* Temperature
* Integrated line intensity at 300 K
* Partition function at 300 K
* Partition function at designated temperature
* Upper state degeneracy
* Upper level energy in Joules
* Lower level energy in Joules
* Degrees of freedom
"""
if isinstance(mol_tag, str):
query = JPLSpec.query_lines_async(
min_frequency=(transition_freq - (1 * u.GHz)),
max_frequency=(transition_freq + (1 * u.GHz)),
molecule=mol_tag,
parse_name_locally=True,
get_query_payload=True)
res = dict(query)
# python request payloads aren't stable (could be
# dictionary or list)
# depending on the version, so make
# sure to check back from time to time
if len(res['Mol']) > 1:
raise JPLSpecQueryFailed(("Ambiguous choice for molecule,\
more than one molecule was found for \
the given mol_tag. Please refine \
your search to one of the following tags\
{} by using JPLSpec.get_species_table()\
(as shown in JPLSpec documentation)\
to parse their names and choose your \
molecule of interest, or refine your\
regex to be more specific (hint '^name$'\
will match 'name' exactly with no\
ambiguity).").format(res['Mol']))
else:
mol_tag = res['Mol'][0]
query = JPLSpec.query_lines(
min_frequency=(transition_freq - (1 * u.GHz)),
max_frequency=(transition_freq + (1 * u.GHz)),
molecule=mol_tag)
freq_list = query['FREQ']
if freq_list[0] == 'Zero lines we':
raise JPLSpecQueryFailed(
("Zero lines were found by JPLSpec in a +/- 1 GHz "
"range from your provided transition frequency for "
"molecule tag {}.").format(mol_tag))
t_freq = min(list(freq_list.quantity),
key=lambda x: abs(x - transition_freq))
data = query[query['FREQ'] == t_freq.value]
df = int(data['DR'].data)
lgint = float(data['LGINT'].data)
lgint = 10**lgint * u.nm * u.nm * u.MHz
elo = float(data['ELO'].data) / u.cm
gu = float(data['GUP'].data)
cat = JPLSpec.get_species_table()
mol = cat[cat['TAG'] == mol_tag]
temp_list = cat.meta['Temperature (K)'] * u.K
part = list(mol['QLOG1', 'QLOG2', 'QLOG3', 'QLOG4', 'QLOG5', 'QLOG6',
'QLOG7'][0])
temp = temp_estimate
f = np.interp(np.log(temp.value), np.log(temp_list.value[::-1]),
np.log(part[::-1]))
f = np.exp(f)
partition = 10**(f)
part300 = 10**(float(mol['QLOG1'].data))
# yields in 1/cm
energy = elo + (t_freq.to(1 / u.cm, equivalencies=u.spectral()))
energy_J = energy.to(u.J, equivalencies=u.spectral())
elo_J = elo.to(u.J, equivalencies=u.spectral())
quantities = [
t_freq, temp, lgint, part300, partition, gu, energy_J, elo_J, df,
mol_tag
]
names = [
't_freq', 'temp', 'lgint300', 'partfn300', 'partfn', 'dgup',
'eup_J', 'elo_J', 'degfreedom', 'mol_tag'
]
# names = ('Transition frequency',
# 'Temperature',
# 'Integrated line intensity at 300 K',
# 'Partition function at 300 K',
# 'Partition function at designated temperature',
# 'Upper state degeneracy',
# 'Upper level energy in Joules',
# 'Lower level energy in Joules',
# 'Degrees of freedom', 'Molecule Identifier')
result = cls.from_dict(dict(zip(names, quantities)))
return result
def query_object_async(self,
wavelength_range=None,
wavelength_type='',
wavelength_accuracy=None,
element_spectrum=None,
minimal_abundance=None,
depl_factor=None,
lower_level_energy_range=None,
upper_level_energy_range=None,
nmax=None,
multiplet=None,
transitions=None,
show_fine_structure=None,
show_auto_ionizing_transitions=None,
output_columns=('spec', 'type', 'conf', 'term',
'angm', 'prob', 'ener')):
"""
Returns
-------
response : `requests.Response`
The HTTP response returned from the service.
"""
if self._default_form_values is None:
response = self._request("GET",
url=self.FORM_URL,
data={},
timeout=self.TIMEOUT)
bs = BeautifulSoup(response.text)
form = bs.find('form')
self._default_form_values = self._get_default_form_values(form)
default_values = self._default_form_values
wltype = (wavelength_type or default_values.get('air', '')).lower()
if wltype in ('air', 'vacuum'):
air = wltype.capitalize()
else:
raise ValueError('parameter wavelength_type must be either "air" '
'or "vacuum".')
wlrange = wavelength_range or []
if len(wlrange) not in (0, 2):
raise ValueError('Length of `wavelength_range` must be 2 or 0, '
'but is: {}'.format(len(wlrange)))
if not is_valid_transitions_param(transitions):
raise ValueError(
'Invalid parameter "transitions": {0!r}'.format(transitions))
if transitions is None:
_type = self._default_form_values.get('type')
type2 = self._default_form_values.get('type2')
else:
s = str(transitions)
if len(s.split(',')) > 1:
_type = 'Sel'
type2 = s.split(',')
else:
_type = s
type2 = ''
# convert wavelengths in incoming wavelength range to Angstroms
wlrange_in_angstroms = (wl.to(u.Angstrom,
equivalencies=u.spectral()).value
for wl in wlrange)
lower_level_erange = lower_level_energy_range
if lower_level_erange is not None:
lower_level_erange = lower_level_erange.to(
u.cm**-1, equivalencies=u.spectral()).value()
upper_level_erange = upper_level_energy_range
if upper_level_erange is not None:
upper_level_erange = upper_level_erange.to(
u.cm**-1, equivalencies=u.spectral()).value()
input = {
'wavl': '-'.join(map(str, wlrange_in_angstroms)),
'wave': 'Angstrom',
'air': air,
'wacc': wavelength_accuracy,
'elmion': element_spectrum,
'abun': minimal_abundance,
'depl': depl_factor,
'elo': lower_level_erange,
'ehi': upper_level_erange,
'ener': 'cm^-1',
'nmax': nmax,
'term': multiplet,
'type': _type,
'type2': type2,
'hydr': show_fine_structure,
'auto': show_auto_ionizing_transitions,
'form': output_columns,
'tptype': 'as_a'
}
response = self._submit_form(input)
return response
def test_equiv_compose():
composed = u.m.compose(equivalencies=u.spectral())
assert any([u.Hz] == x.bases for x in composed)
def blackbody_nu(in_x, temperature):
"""Calculate blackbody flux per steradian, :math:`B_{\\nu}(T)`.
.. note::
Use `numpy.errstate` to suppress Numpy warnings, if desired.
.. warning::
Output values might contain ``nan`` and ``inf``.
Parameters
----------
in_x : number, array-like, or `~astropy.units.Quantity`
Frequency, wavelength, or wave number.
If not a Quantity, it is assumed to be in Hz.
temperature : number, array-like, or `~astropy.units.Quantity`
Blackbody temperature.
If not a Quantity, it is assumed to be in Kelvin.
Returns
-------
flux : `~astropy.units.Quantity`
Blackbody monochromatic flux in
:math:`erg \\; cm^{-2} s^{-1} Hz^{-1} sr^{-1}`.
Raises
------
ValueError
Invalid temperature.
ZeroDivisionError
Wavelength is zero (when converting to frequency).
"""
# Convert to units for calculations, also force double precision
with u.add_enabled_equivalencies(u.spectral() + u.temperature()):
freq = u.Quantity(in_x, u.Hz, dtype=np.float64)
temp = u.Quantity(temperature, u.K, dtype=np.float64)
# Check if input values are physically possible
if np.any(temp < 0):
raise ValueError(f'Temperature should be positive: {temp}')
if not np.all(np.isfinite(freq)) or np.any(freq <= 0):
warnings.warn('Input contains invalid wavelength/frequency value(s)',
AstropyUserWarning)
log_boltz = const.h * freq / (const.k_B * temp)
boltzm1 = np.expm1(log_boltz)
if _has_buggy_expm1:
# Replace incorrect nan results with infs--any result of 'nan' is
# incorrect unless the input (in log_boltz) happened to be nan to begin
# with. (As noted in #4393 ideally this would be replaced by a version
# of expm1 that doesn't have this bug, rather than fixing incorrect
# results after the fact...)
boltzm1_nans = np.isnan(boltzm1)
if np.any(boltzm1_nans):
if boltzm1.isscalar and not np.isnan(log_boltz):
boltzm1 = np.inf
else:
boltzm1[np.where(~np.isnan(log_boltz) & boltzm1_nans)] = np.inf
# Calculate blackbody flux
bb_nu = (2.0 * const.h * freq ** 3 / (const.c ** 2 * boltzm1))
flux = bb_nu.to(FNU, u.spectral_density(freq))
return flux / u.sr # Add per steradian to output flux unit
def _(attr, results):
return set(
it for it in results if it.wave.wavemax is not None and
attr.min <= it.wave.wavemax.to(u.angstrom, equivalencies=u.spectral())
and it.wave.wavemin is not None and
attr.max >= it.wave.wavemin.to(u.angstrom, equivalencies=u.spectral()))
def make_obsdata_from_model(model_filename,
model_type='tlusty',
model_params=None,
output_filebase=None,
output_path=None,
show_plot=False):
"""
Create the necessary data files (.dat and spectra) from a
stellar model atmosphere model to use as the unreddened
comparsion star in the measure_extinction package
Parameters
----------
model_filename: string
name of the file with the stellar atmosphere model spectrum
model_type: string [default = 'tlusty']
model type
model_params: dict of {type: value}
model parameters
e.g., {'Teff': 10000.0, 'logg': 4.0, 'Z': 1, 'vturb': 2.0}
output_filebase: string
base for the output files
E.g., output_filebase.dat and output_filebase_stis.fits
output_path: string
path to use for output files
show_plot: boolean
show a plot of the original and rebinned spectra/photometry
"""
if output_filebase is None:
output_filebase = '%s_standard' % (model_filename)
if output_path is None:
output_path = '/home/kgordon/Python_git/extstar_data/'
allowed_model_types = ['tlusty']
if model_type not in allowed_model_types:
raise ValueError("%s not an allowed model type" % (model_type))
# read in the model spectrum
mspec = ascii.read(model_filename,
format='no_header',
fast_reader={'exponent_style': 'D'},
names=['Freq', 'SFlux'])
# error in file where the exponent 'D' is missing
# means that SFlux is read in as a string
# solution is to remove the rows with the problem and replace
# the fortran 'D' with an 'E' and then convert to floats
if mspec['SFlux'].dtype != np.float:
indxs = [k for k in range(len(mspec)) if 'D' not in mspec['SFlux'][k]]
if len(indxs) > 0:
indxs = [k for k in range(len(mspec)) if 'D' in mspec['SFlux'][k]]
mspec = mspec[indxs]
new_strs = [cval.replace('D', 'E') for cval in mspec['SFlux'].data]
mspec['SFlux'] = new_strs
mspec['SFlux'] = mspec['SFlux'].astype(np.float)
# set the units
mspec['Freq'].unit = u.Hz
mspec['SFlux'].unit = u.erg / (u.s * u.cm * u.cm * u.Hz)
# now extract the wave and flux colums
mfreq = mspec['Freq'].quantity
mwave = mfreq.to(u.angstrom, equivalencies=u.spectral())
mflux = mspec['SFlux'].quantity.to(u.erg /
(u.s * u.cm * u.cm * u.angstrom),
equivalencies=u.spectral_density(mfreq))
# rebin to R=5000 for speed
# use a wavelength range that spans FUSE to Spitzer IRS
wave_r5000, flux_r5000, npts_r5000 = rebin_spectrum(
mwave.value, mflux.value, 5000, [912., 500000.])
# save the full spectrum to a binary FITS table
otable = Table()
otable['WAVELENGTH'] = Column(wave_r5000, unit=u.angstrom)
otable['FLUX'] = Column(flux_r5000,
unit=u.erg / (u.s * u.cm * u.cm * u.angstrom))
otable['SIGMA'] = Column(flux_r5000 * 0.0,
unit=u.erg / (u.s * u.cm * u.cm * u.angstrom))
otable['NPTS'] = Column(npts_r5000)
otable.write("%s/Models/%s_full.fits" % (output_path, output_filebase),
overwrite=True)
# dictionary to saye names of spectroscopic filenames
specinfo = {}
# create the ultraviolet HST/STIS mock observation
# first create the spectrum convolved to the STIS low resolution
# Resolution approximately 1000
stis_fwhm_pix = 5000. / 1000.
g = Gaussian1DKernel(stddev=stis_fwhm_pix / 2.355)
# Convolve data
nflux = convolve(otable['FLUX'].data, g)
stis_table = Table()
stis_table['WAVELENGTH'] = otable['WAVELENGTH']
stis_table['FLUX'] = nflux
stis_table['NPTS'] = otable['NPTS']
stis_table['STAT-ERROR'] = Column(np.full((len(stis_table)), 1.0))
stis_table['SYS-ERROR'] = otable['SIGMA']
# UV STIS obs
rb_stis_uv = merge_stis_obsspec([stis_table], waveregion='UV')
rb_stis_uv['SIGMA'] = rb_stis_uv['FLUX'] * 0.0
stis_uv_file = "%s_stis_uv.fits" % (output_filebase)
rb_stis_uv.write("%s/Models/%s" % (output_path, stis_uv_file),
overwrite=True)
specinfo['STIS'] = stis_uv_file
# Optical STIS obs
rb_stis_opt = merge_stis_obsspec([stis_table], waveregion='Opt')
rb_stis_opt['SIGMA'] = rb_stis_opt['FLUX'] * 0.0
stis_opt_file = "%s_stis_opt.fits" % (output_filebase)
rb_stis_opt.write("%s/Models/%s" % (output_path, stis_opt_file),
overwrite=True)
specinfo['STIS_Opt'] = stis_opt_file
# Spitzer IRS mock observation
# Resolution approximately 100
lrs_fwhm_pix = 5000. / 100.
g = Gaussian1DKernel(stddev=lrs_fwhm_pix / 2.355)
# Convolve data
nflux = convolve(otable['FLUX'].data, g)
lrs_table = Table()
lrs_table['WAVELENGTH'] = otable['WAVELENGTH']
lrs_table['FLUX'] = nflux
lrs_table['NPTS'] = otable['NPTS']
lrs_table['ERROR'] = Column(np.full((len(lrs_table)), 1.0))
rb_lrs = merge_irs_obsspec([lrs_table])
rb_lrs['SIGMA'] = rb_lrs['FLUX'] * 0.0
lrs_file = "%s_irs.fits" % (output_filebase)
rb_lrs.write("%s/Models/%s" % (output_path, lrs_file), overwrite=True)
specinfo['IRS'] = lrs_file
# compute photometry
# band_path = "%s/Band_RespCurves/" % output_path
john_bands = ['U', 'B', 'V', 'R', 'I', 'J', 'H', 'K']
john_fnames = ["John%s.dat" % (cband) for cband in john_bands]
hst_bands = [
'HST_WFC3_UVIS1_F275W', 'HST_WFC3_UVIS1_F336W', 'HST_WFC3_UVIS1_F475W',
'HST_WFC3_UVIS1_F814W', 'HST_WFC3_IR_F110W', 'HST_WFC3_IR_F160W',
'HST_ACS_WFC1_F475W', 'HST_ACS_WFC1_F814W', 'HST_WFPC2_4_F170W'
]
hst_fnames = ['']
# spitzer_bands = ['IRAC1', 'IRAC2', 'IRAC3', 'IRAC4', 'IRS15', 'MIPS24']
# spitzer_fnames = ["{}/{}.dat".format(band_path, cband)
# for cband in spitzer_bands]
bands = john_bands + hst_bands
band_fnames = john_fnames + hst_fnames
# bands = john_bands
# band_fnames = john_fnames
bandinfo = get_phot(wave_r5000, flux_r5000, bands, band_fnames)
# create the DAT file
dat_filename = "%s/Models/%s.dat" % (output_path, output_filebase)
header_info = [
"# obsdata created from %s model atmosphere" % model_type,
"# %s" % (output_filebase),
"# file created by make_obsdata_from_model.py",
"model_type = %s" % model_type
]
write_dat_file(dat_filename,
bandinfo,
specinfo,
modelparams=model_params,
header_info=header_info)
if show_plot:
fig, ax = plt.subplots(figsize=(13, 10))
# indxs, = np.where(npts_r5000 > 0)
ax.plot(wave_r5000 * 1e-4, flux_r5000, 'b-')
ax.plot(bandinfo.waves, bandinfo.fluxes, 'ro')
indxs, = np.where(rb_stis_uv['NPTS'] > 0)
ax.plot(rb_stis_uv['WAVELENGTH'][indxs].to(u.micron),
rb_stis_uv['FLUX'][indxs], 'm-')
indxs, = np.where(rb_stis_opt['NPTS'] > 0)
ax.plot(rb_stis_opt['WAVELENGTH'][indxs].to(u.micron),
rb_stis_opt['FLUX'][indxs], 'g-')
indxs, = np.where(rb_lrs['NPTS'] > 0)
ax.plot(rb_lrs['WAVELENGTH'][indxs].to(u.micron),
rb_lrs['FLUX'][indxs], 'c-')
ax.set_xscale('log')
ax.set_yscale('log')
plt.show()
def download_cutouts(sbid, username, password, destination_dir, num_channels, data_product_sub_type):
print ("\n\n** Finding images and image cubes for scheduling block {} ... \n\n".format(sbid))
sbid_multi_channel_query = "SELECT TOP 1000 * FROM ivoa.obscore where obs_id='" + str(sbid) \
+ "' and dataproduct_subtype='" + str(data_product_sub_type) \
+ "' and em_xel > 1 and dataproduct_type = 'cube'"
# create async TAP query and wait for query to complete
result_file_path = casda.async_tap_query(sbid_multi_channel_query, username, password, destination_dir)
image_cube_votable = parse(result_file_path, pedantic=False)
results_array = image_cube_votable.get_table_by_id('results').array
# 3) For each of the image cubes, query datalink to get the secure datalink details
print ("\n\n** Retrieving datalink for each image and image cube...\n\n")
authenticated_id_tokens = []
for image_cube_result in results_array:
image_cube_id = image_cube_result['obs_publisher_did'].decode('utf-8')
async_url, authenticated_id_token = casda.get_service_link_and_id(image_cube_id, username,
password,
service='cutout_service',
destination_dir=destination_dir)
if authenticated_id_token is not None:
authenticated_id_tokens.append([authenticated_id_token, image_cube_result])
if len(authenticated_id_tokens) == 0:
print ("No image cubes for scheduling_block_id " + str(sbid))
return 1
# For each image cube, slice by channels using num_channels specified by the user.
band_list = []
job_locations = []
for entry in authenticated_id_tokens:
auth_id_token = entry[0]
ic = entry[1]
em_xel = ic['em_xel']
em_min = ic['em_min'] * u.m
em_max = ic['em_max'] * u.m
min_freq = em_max.to(u.Hz, equivalencies=u.spectral())
max_freq = em_min.to(u.Hz, equivalencies=u.spectral())
step_size = num_channels
if step_size > em_xel:
step_size = em_xel
hz_per_channel = (max_freq - min_freq) / em_xel
pos = em_xel
channel_blocks = math.ceil(em_xel / num_channels)
for b in range(int(channel_blocks)):
f1 = get_freq_at_pos(pos, min_freq, hz_per_channel)
pos -= step_size
f2 = get_freq_at_pos(pos, min_freq, hz_per_channel)
pos -= 1 # do not overlap channels between image cubes
wavelength1 = f1.to(u.m, equivalencies=u.spectral())
wavelength2 = f2.to(u.m, equivalencies=u.spectral())
band = str(wavelength1.value) + " " + str(wavelength2.value)
band_list.append(band)
# create job for given band params
job_location = casda.create_async_soda_job([auth_id_token])
casda.add_params_to_async_job(job_location, 'BAND', band_list)
job_locations.append(job_location)
# run all jobs and download
casda.run_async_jobs_and_download(job_locations, destination_dir)
return 0