trident.spectrum_generator.SpectrumGenerator

class trident.spectrum_generator.SpectrumGenerator(instrument=None, lambda_min=None, lambda_max=None, n_lambda=None, dlambda=None, lsf_kernel=None, line_database='lines.txt', ionization_table=None, bin_space='wavelength')[source]

Preferred class for generating, storing, and plotting absorption-line spectra. SpectrumGenerator is a subclass of yt’s AbsorptionSpectrum class with additional functionality like line lists, post-processing to include Milky Way foreground, quasar backgrounds, applying line-spread functions, and plotting.

User first specifies the telescope/instrument used for generating spectra (e.g. ‘COS’ for the Cosmic Origins Spectrograph aboard the Hubble Space Telescope). This can be done by naming the Instrument, or manually setting all of the spectral characteristics including lambda_min, lambda_max, lsf_kernel, and n_lambda or dlambda. If none of these arguments are set, defaults to ‘COS’ as the default instrument covering 1150-1450 Angstroms with a binsize (dlambda) of 0.1 Angstroms.

Once a SpectrumGenerator has been initialized, pass it LightRay objects using make_spectrum to actually generate the spectra themselves. Then one can post-process, plot, or save them using add_milky_way_foreground, add_qso_spectrum, apply_lsf, save_spectrum, and plot_spectrum.

Parameters

Instrument:

string, optional

The spectrograph to use. Currently, the only named options are different observing modes of the Cosmic Origins Spectrograph ‘COS’: ‘COS-G130M’, ‘COS-G160M’, and ‘COS-G140L’ as well as ‘COS’ which aliases to ‘COS-G130M’. These automatically set the lambda_min, lambda_max, dlambda and lsf_kernel``s appropriately. If you're going to set ``lambda_min, lambda_max, et al manually, leave this set to None. Default: None

Lambda_min:

float, YTQuantity, or ‘auto’

lower wavelength bound in angstroms or velocity bound in km/s (if bin_space set to ‘velocity’). If set to ‘auto’, the lower bound will be automatically adjusted to encompass all absorption lines. The window will not be expanded for continuum features, only absorption lines.

Lambda_max:

float, YTQuantity, or ‘auto’

upper wavelength bound in angstroms or velocity bound in km/s (if bin_space set to ‘velocity’). If set to ‘auto’, the upper bound will be automatically adjusted to encompass all absorption lines. The window will not be expanded for continuum features, only absorption lines.

N_lambda:

int

The number of bins in the spectrum (inclusive), so if extrema = 10 and 20, and dlambda (binsize) = 1, then n_lambda = 11. Default: None

Dlambda:

float

size of the wavelength bins in angstroms or velocity bins in km/s. Default: None

Bin_space:

‘wavelength’ or ‘velocity’

Sets the dimension in which spectra are created. If set to wavelength, the resulting spectra are flux (or tau) vs. observed wavelength. If set to velocity, the spectra are flux vs. velocity offset from the rest wavelength of the absorption line. Default: wavelength

Lsf_kernel:

string, optional

The filename for the LSF kernel. Files are found in trident.__path__/data/lsf_kernels or current working directory. Only necessary if you are applying an LSF to the spectrum in postprocessing. Default: None

Line_database:

string or LineDatabase, optional

A text file listing the various lines to insert into the line database, or a LineDatabase object in memory. The line database provides a list of all possible lines that could be added to the spectrum. For a text file, it should have 4 tab-delimited columns of name (e.g. MgII), wavelength in angstroms, gamma of transition, and f-value of transition. See example datasets in trident.path/data/line_lists for examples. Default: lines.txt

Ionization_table:

hdf5 file, optional

An HDF5 file used for computing the ionization fraction of the gas based on its density, temperature, metallicity, and redshift. If set to None, will use the ion table defined in your Trident config file. Default: None

Example

Create a one-zone ray, and generate a COS spectrum from that ray.

>>> import trident
>>> ray = trident.make_onezone_ray()
>>> sg = trident.SpectrumGenerator('COS')
>>> sg.make_spectrum(ray)
>>> sg.plot_spectrum('spec_raw.png')

Create a one-zone ray at redshift 0.5, and generate a spectrum with 1 angstrom spectral bins from 2000-4000 angstroms, then post-process by adding a MW foreground a QSO background at z=0.5 and add a boxcar line spread function of 100 angstroms width. Plot it and save the figure to ‘spec_final.png’.

>>> import trident
>>> ray = trident.make_onezone_ray(redshift=0.5)
>>> sg = trident.SpectrumGenerator(lambda_min=2000, lambda_max=4000,
... dlambda=1)
>>> sg.make_spectrum(ray)
>>> sg.add_qso_spectrum(emitting_redshift=.5)
>>> sg.add_milky_way_foreground()
>>> sg.apply_lsf(function='boxcar', width=100)
>>> sg.plot_spectrum('spec_final.png')

Methods

`__init__`
`add_continuum`	Add a continuum feature that follows a power-law.
`add_gaussian_noise`	Postprocess a spectrum to add gaussian random noise of a given SNR.
`add_line`	Add an absorption line to the list of lines included in the spectrum.
`add_line_to_database`	Adds desired line to the current `LineDatabase` object.
`add_milky_way_foreground`	Postprocess a spectrum to add a Milky Way foreground.
`add_noise_vector`	Add an array of noise to the spectrum.
`add_qso_spectrum`	Postprocess a spectrum to add a QSO spectrum background.
`apply_lsf`	Postprocess a spectrum to apply a line spread function.
`clear_spectrum`	Clear the current spectrum in the SpectrumGenerator.
`error_func`	Approximate the flux error for a spectrum.
`load_spectrum`	Load data arrays into an existing spectrum object.
`make_spectrum`	Make a spectrum from ray data depositing the desired lines.
`plot_spectrum`	Plot the current spectrum and save to disk.
`save_spectrum`	Save the current spectrum data to an output file.

Attributes

`current_tau_field`	This is the optical depth array for the current absorption line being deposited.
`lambda_field`	The lambda field.
`tau_field`	This is the total optical depth of all lines and continua.