Getting Started

Spectacle is designed to facilitate the creation of complex spectral models. It is built on the Astropy modeling module. It can create representations of spectral data in wavelength, frequency, or velocity space, with any number of line components. These models can then be fit to data for use in individual ion reduction, or characterization of spectra as a whole.

Creating a spectral model

The primary class is the Spectral1D. This serves as the central object through which the user will design their model, and so exposes many parameters to the user.

Spectral1D models are initialized with several descriptive properties:

Attribute	Description
z	This is the redshift of the spectrum. It can either be a single numerical value, or an array describing the redshift at each e.g. velocity bin. Note if the user provides an array, the length of the redshift array must match the length of the dispersion array used as input to the model. Default: 0
rest_wavelength	The wavelength at which transformations from wavelength space to velocity space will be performed. Default: 0 Angstrom
output	Describes the type of data the spectrum model will produce. This can be one of flux, flux_decrement, or optical_depth. Default: `flux`
continuum	A FittableModel1D or single numeric value representing the continuum for the spectral model. Default: 0
lsf	The line spread function to be applied to the model. Users can provided an LSFModel, a Kernel1D, or a string indicating either cos for the COS LSF, or guassian for a Gaussian LSF. In the latter case, the user should provide key word arguments as parameters for the Gaussian profile.
lines	The set of lines to be added to the spectrum. This information is passed to the OpticalDepth1D initializer. This can either be a single OpticalDepth1D instance, a list of OpticalDepth1D instances; a single string representing the name of an ion (e.g. “HI1216”), a list of such strings; a single Quantity value representing the rest wavelength of an ion, or a list of such values.

The Spectral1D does not require that any lines be provided initially. In that case, it will just generate data only considering the continuum and other properties.

Providing lines to the initializer

As mentioned in the table above, lines can be added by passing a set of OpticalDepth1D instances, ion name strings, or rest wavelength Quantity objects to the initializer.

Using a set of OpticalDepth1D instances:

line = OpticalDepth1D("HI1216", v_doppler=50 * u.km/u.s, column_density=14)
line2 = OpticalDepth1D("HI1216", delta_v=100 * u.km/u.s)
spec_mod = Spectral1D([line, line2])

Using ion name strings:

spec_mod = Spectral1D(["HI1216", "OVI1032"])

Using rest wavelength Quantity objects:

spec_mod = Spectral1D([1216 * u.Angstrom, 1032 * u.Angstrom])

Adding lines after model creation

Likewise, the user can add a line to an already made spectral model by using the with_line() method, and provide to it information accepted by the OpticalDepth1D class

>>> from spectacle import Spectral1D
>>> import astropy.units as u
>>> spec_mod = Spectral1D([1216 * u.AA])
>>> spec_mod = spec_mod.with_line("HI1216", v_doppler=50 * u.km/u.s, column_density=14)
>>> print(spec_mod)  
Model: Spectral1D
Inputs: ('x',)
Outputs: ('y',)
Model set size: 1
Parameters:
    amplitude_0 z_1 lambda_0_2 f_value_2   gamma_2   v_doppler_2 column_density_2 delta_v_2 delta_lambda_2 lambda_0_3 f_value_3   gamma_3   v_doppler_3 column_density_3 delta_v_3 delta_lambda_3 z_5
                     Angstrom                           km / s                      km / s     Angstrom     Angstrom                           km / s                      km / s     Angstrom
    ----------- --- ---------- --------- ----------- ----------- ---------------- --------- -------------- ---------- --------- ----------- ----------- ---------------- --------- -------------- ---
            0.0 0.0  1215.6701    0.4164 626500000.0        10.0             13.0       0.0            0.0  1215.6701    0.4164 626500000.0        50.0             14.0       0.0            0.0 0.0