qusp.spectrum module

Provides classes to represent functions of wavelength.

Examples

Construct a Spectrum object from wave, flux, and ivar arrays:

>>> spectrum = qusp.spectrum.Spectrum(wave, flux, ivar)

Get the mean flux between wave_min and wave_max:

>>> spectrum.mean_flux(wave_min, wave_max)

Get the median signal to noise between wave_min and wave_max:

>>> spectrum.median_signal_to_noise(wave_min, wave_max)

Load the combined spectrum of a qsub.target.Target object, target:

filename = 'spPlate-%s-%s.fits' % (target['plate'], target['mjd'])
spplate = fits.open(os.path.join(paths.boss_path, str(target['plate']), filename))
combined = qusp.read_combined_spectrum(spplate, target)
class qusp.spectrum.BOSSSpectrum(wavelength, flux, ivar, wavelengths_units=<Mock id='140482188747280'>, flux_units=None, extrapolated_value=None)

Bases: object

Represents a BOSS co-added spectrum.

Parameters:
create_corrected(correction)
find_pixel(wavelength, clip=False)

Returns the corresponding pixel index of the specified wavelength.

Parameters:
  • wavelength (float) – value
  • clip (bool) – if wavelength is out of range, return 0, or npixels-1
Returns:

pixel index
Return type:

pixelIndex (int)
mean_flux(min_wavelength, max_wavelength, ivar_weighting=True)

Returns the mean flux between the specified wavelengths. Use ivar_weighting=False to turn ignore weights.

Parameters:
  • min_wavelength (float) – minimum wavelength for mean flux calculation range.
  • max_wavelength (float) – maximum wavelength for mean flux calculation range.
  • ivar_weighting (bool, optional) – Whether or not to weight calculation using inverse variance.
Returns:

the mean flux between min_wavelength and max_wavelength.
median_signal_to_noise(min_wavelength, max_wavelength)

Returns the median signal to noise ratio between the specified wavelengths.

Parameters:
  • min_wavelength (float) – minimum wavelength for median flux calculation range.
  • max_wavelength (float) – maximum wavelength for median flux calculation range.
Returns:

the median flux between min_wavelength and max_wavelength.
Return type:

median (float)
trim_range(wave_min, wave_max, clip=True)

Returns a BOSSSpectrum object trimmed to the specified range.

Parameters:
  • wave_min (float) – wavelength range lower bound
  • wave_max (float) – wavelength range upper bound
Returns:

A BOSSSpectrum
Raises:

ValueError – if no pixels in specified range
class qusp.spectrum.SpectralFluxDensity(wavelength, flux, wavelengths_units=<Mock id='140482189143568'>, flux_units=None, extrapolated_value=None)

Bases: qusp.spectrum.WavelengthFunction

Represents a spectral flux density as a function of wavelength.

Initializes a spectral flux density using tabulated flux values at specified wavelengths. See the documentation of WavelengthFunction for details. The default flux unit is 1e-17 erg/(s*cm^2*Ang), which is available as SpectralFluxDensity.fiducialFluxUnit, but other units can be specified.

Parameters:
  • wavelength (numpy.ndarray) – tabulated wavelength values
  • flux (numpy.ndarray) – tabulated flux values
  • wavelengths_units (astropy.units.Quantity) – wavelength value units
  • flux_units (astropy.units.Quantity) – flux value units
  • extrapolated_value (float, optional) –
create_redshifted(new_z, old_z=0.0, preserve_wavelengths=False)

Returns a new SpectralFluxDensity whose wavelengths and fluxes have been rescaled for the transformation from old_z to new_z. If preserve_wavelengths is True and an extrapolated_value has been set, then the rescaled spectrum will be resampled to the original wavelengths. Otherwise, the new spectrum will be tabulated on the redshifted grid.

Parameters:
  • new_z (float) – redshift to rescale to
  • old_z (float, optional) – original redshift to rescale from
  • preserve_wavelengths (bool) – preserve wavelength grid, otherwise create redshifted grid
Returns:

rescaled spectrum (qusp.spectrum.SpectralFluxDensity)
Raises:

RuntimeError – if preserve_wavelengths is True and no extrapolated_value has been set
create_rescaled(sdss_band, ab_magnitude)
Parameters:
  • sdss_band (string) – SDSS band (identified by a character ‘u’,’g’,’r’,’i’,’z’)
  • ab_magnitude (float) – AB magnitude to match
Returns:

rescaled spectrum (qusp.spectrum.SpectralFluxDensity)
Raises:

RuntimeError – in case our spectrum does not fully cover the band.
fiducialFluxUnit

1e-17 erg/(s*cm^2*Ang)

get_ab_magnitudes()

Returns a dictionary of AB magnitudes calculated in each SDSS filter. Magnitude values of None are returned when our spectrum has no extrapolated_value set and a filter extends beyond our tabulated wavelengths.

get_filtered_rates(filter_curves, wavelength_step=1.0)

Returns the counting rates in photons/(s*cm^2) when our spectral flux density is filtered by the specified curves. The curves should be specified as a dictionary of WavelengthFunctions and the results will also be a dictionary of floats using the same keys. Rates of None are returned when our spectrum has no extrapolated_value set and a filter extends beyond our tabulated wavelengths.

Parameters:filter_curves (dict) – dictionary of WavelengthFunctions
sdss_filter_curves = None
sdss_filter_rates = None
class qusp.spectrum.Spectrum(wavelength, flux, ivar)

Bases: object

Represents a BOSS co-added spectrum.

Parameters:
find_pixel(wavelength)

Returns the corresponding pixel index of the specified wavelength.

Parameters:wavelength (float) – value
Returns:pixel index
Return type:pixelIndex (int)
mean_flux(min_wavelength, max_wavelength, ivar_weighting=True)

Returns the mean flux between the specified wavelengths. Use ivar_weighting=False to turn ignore weights.

Parameters:
  • min_wavelength (float) – minimum wavelength for mean flux calculation range.
  • max_wavelength (float) – maximum wavelength for mean flux calculation range.
  • ivar_weighting (bool, optional) – Whether or not to weight calculation using inverse variance.
Returns:

the mean flux between min_wavelength and max_wavelength.
median_signal_to_noise(min_wavelength, max_wavelength)

Returns the median signal to noise ratio between the specified wavelengths.

Parameters:
  • min_wavelength (float) – minimum wavelength for median flux calculation range.
  • max_wavelength (float) – maximum wavelength for median flux calculation range.
Returns:

the median flux between min_wavelength and max_wavelength.
Return type:

median (float)
class qusp.spectrum.WavelengthFunction(wavelength, values, wavelengths_units=<Mock id='140482189143056'>, value_units=None, extrapolated_value=None)

Bases: object

Represents an arbitrary function of wavelength.

Initializes a function of wavelength using tabulated values at specified wavelengths. The default wavelength units are angstroms but other units can be specified. Optional value units can also be specified but are not required. The input wavelengths must be increasing. The input wavelength and value arrays must have the same size. If either is already a numpy array, no internal copy is made (except when conversion to Angstroms is needed) so these are lightweight objects but be aware of possible side effects.

Parameters:
  • wavelength (np.ndarray) – tabulated wavelength values
  • values (np.ndarray) – tabulated values
  • wavelengths_units (astropy.units.Quantity) – wavelength value units
  • value_units (astropy.units.Quantity, optional) – value units
  • extrapolated_value (float, optional) –
get_model()

Returns a model for interpolating within our tabulated wavelength function values. If an extrapolated_value was provided to the constructor, the model will use this for any wavelengths outside the tabulated grid.

Returns:model (scipy.interpolate.interp1d)
get_resampled_values(wavelength, wavelengths_units=<Mock id='140482189143184'>)

Returns a numpy array of values resampled at the specified wavelengths (which do not need to be sorted). The default wavelength units are angstroms but other units can be specified.

Parameters:
  • wavelength (numpy.ndarray) – wavelengths to resample at
  • wavelengths_units (astropy.Units.Quantity) – wavelength value units
Returns:

resampled values (numpy.ndarray)
Raises:

RuntimeError – if resampling would require an extrapolation but no extrapolated_value was provided to the constructor.
classmethod load_from_text_file(filename, wavelength_column=0, values_column=1, wavelengths_units=<Mock id='140482189143376'>, extrapolated_value=None)

Returns a new WavelengthFunction (or subclass of WavelengthFunction) from the specified text file. Any comment lines beginning with ‘#’ are ignored. Uses the specified columns for the wavelength and values. Additional columns are allowed and silently ignored. The default wavelength units are Angstroms but other units can be specified. Refer to the WavelengthFunction constructor for details on extrapolated_value.

Parameters:filename (string) –
save_to_text_file(filename)

Writes a text file containing two columns: wavelength and values.

Parameters:filename (string) –
qusp.spectrum.load_sdss_filter_curves(which_column=1)

Loads SDSS filter curves from a standard location within this module. The default which_column=1 corresponds to curves of the quantum efficiency on the sky looking through 1.3 airmasses at APO for a point source. Values of 2-4 are also possible but probably not what you want. Consult the filter data file headers for details.

qusp.spectrum.read_combined_spectrum(spplate, fiber)

Returns the combined spectrum of the specified fiber from the provided spPlate.

Parameters:
Returns:

a Spectrum object of fiber of spplate.
Return type:

spectrum (Spectrum)
qusp.spectrum.read_lite_spectrum(spec)

Returns the combined spectrum of the specified fiber from the provided spPlate.

Parameters:fiber (qusp.target.Target) – boss target’s fiberid, or a qusp.target.Target object.
Returns:a Spectrum object of fiber of spplate.
Return type:spectrum (Spectrum)