trident.spectrum_generator.plot_spectrum

trident.spectrum_generator.plot_spectrum(wavelength, flux, filename='spectrum.png', lambda_limits=None, flux_limits=None, title=None, label=None, figsize=None, step=False, stagger=0.2, features=None, axis_labels=None)[source]

Plot a spectrum or a collection of spectra and save to disk.

This function wraps some Matplotlib plotting functionality for plotting spectra generated with the SpectrumGenerator. In its simplest form, it accepts a wavelength array consisting of wavelength values and a corresponding flux array consisting of relative flux values, and it plots them and saves to disk.

In addition, it can plot several spectra on the same axes simultaneously by passing a list of arrays to the wavelength, flux arguments (and optionally to the label and step keywords).

Returns the Matplotlib Figure object for further processing.

Parameters

Wavelength:

array of floats or list of arrays of floats

Wavelength values in angstroms. Either as an array of floats in the case of plotting a single spectrum, or as a list of arrays of floats in the case of plotting several spectra on the same axes.

Flux:

array of floats or list of arrays of floats

Relative flux values (from 0 to 1) corresponding to wavelength array. Either as an array of floats in the case of plotting a single spectrum, or as a list of arrays of floats in the case of plotting several spectra on the same axes.

Filename:

string, optional

Output filename of the plotted spectrum. Will be a png file. Default: ‘spectrum.png’

Lambda_limits:

tuple or list of floats, optional

The minimum and maximum of the wavelength range (x-axis) for the plot in angstroms. If specified as None, will use whole lambda range of spectrum. Example: (1200, 1400) for 1200-1400 Angstroms Default: None

Flux_limits:

tuple or list of floats, optional

The minimum and maximum of the flux range (y-axis) for the plot. If specified as None, limits are automatically from [0, 1.1*max(flux)]. Example: (0, 1) for normal flux range before postprocessing. Default: None

Step:

boolean or list of booleans, optional

Plot the spectrum as a series of step functions. Appropriate for plotting processed and noisy data. Use a list of booleans when plotting multiple spectra, where each boolean corresponds to the entry in the wavelength and flux lists.

Title:

string, optional

Optional title for plot Default: None

Label:

string or list of strings, optional

Label for each spectrum to be plotted. Useful if plotting multiple spectra simultaneously. Will automatically trigger a legend to be generated. Default: None

Stagger:

float, optional

If plotting multiple spectra on the same axes, do we offset them in the y direction? If set to None, no. If set to a float, stagger them by the flux value specified by this parameter.

Features:

dict, optional

Include vertical lines with labels to represent certain spectral features. Each entry in the dictionary consists of a key string to be overplot and the value float as to where in wavelength space it will be plot as a vertical line with the corresponding label.

Example: features={‘Ly a’ : 1216, ‘Ly b’ : 1026}

Default: None

Axis_labels:

tuple of strings, optional

Optionally set the axis labels directly. If set to None, defaults to (‘Wavelength [$rmAA$]’, ‘Relative Flux’). Default: None

Returns

Matplotlib Figure object for further processing

Example

Plot a flat spectrum

>>> import numpy as np
>>> import trident
>>> wavelength = np.arange(1200, 1400)
>>> flux = np.ones(len(wavelength))
>>> trident.plot_spectrum(wavelength, flux)

Generate a one-zone ray, create a Lyman alpha spectrum from it, and add gaussian noise to it. Plot both the raw spectrum and the noisy spectrum on top of each other.

>>> import trident
>>> ray = trident.make_onezone_ray(column_densities={'H_p0_number_density':1e21})
>>> sg_final = trident.SpectrumGenerator(lambda_min=1200, lambda_max=1300, dlambda=0.5)
>>> sg_final.make_spectrum(ray, lines=['Ly a'])
>>> sg_final.save_spectrum('spec_raw.h5')
>>> sg_final.add_gaussian_noise(10)
>>> sg_raw = trident.load_spectrum('spec_raw.h5')
>>> trident.plot_spectrum([sg_raw.lambda_field, sg_final.lambda_field],
... [sg_raw.flux_field, sg_final.flux_field], stagger=0, step=[False, True],
... label=['Raw', 'Noisy'], filename='raw_and_noise.png')