AbsorberExtractor

class salsa.AbsorberExtractor(ds_filename, ray_filename, ion_name='H I', cut_region_filters=None, wavelength_center=None, velocity_res=10, spectacle_defaults=None, spectacle_res=None, absorber_min=None, frac=0.8)

Bases: object

Extracts absorbers from a trident lightray for a given ion species. Does This through two methods, by using the SPICE (Simple Procedure for Iterative Cloud Extraction) method and by fitting a synthetic spectra made by trident. Fit is done using spectacle

Parameters

  • ds_filename (str or YT dataset) – Either Path/name of the dataset to be loaded or the dataset itself

  • ray_filename (str or Trident ray) – Path/name of the hdf5 ray file to be loaded or the ray already loaded

  • ion_name (string, optional) – Name of the ion to extract absorbers of Default: “H I”

  • cut_region_filters (list of strings, optional) – a list of filters defined by the way you use Cut Regions in YT Default: None

  • wavelegnth_center (float, optional) – The specific absorption line to look at (in unit Angstrom). None defaults to strongest absorption line for specified ion (using trident’s ion table). Default: None

  • velocity_res (float, optional) – width of velocity bins for spectra. Minimum threshold for combining absorbers in the SPICE method. Default: 10

  • spectacle_res (float, optional) – Set minimum resolution that spectacle will attempt to fit lines to. (in km/s) If None, default to value of velocity_res Default: None

  • spectacle_defaults (dict, optional) – Dictionary passed to spectacle defining default parameters/ranges when fitting absorption lines Deafult: None

  • absorber_min (float, optional) – Minimum Log Column Density that will be used to define an absorber. If None, defaults to either default for specific ion or 13 Default: None

  • frac (float, optional) – Parameter defining what fraction of the number density is being accounted for in each iteration of the SPICE method. Must be a number between 0 and 1. Default: 0.8

Methods Summary

close()

close all opened files, dataset, ray

get_spectacle_absorbers()

Uses spectacle to fit a trident made spectra of the specified ion.

get_spice_absorbers([fields, units_dict])

Use the SPICE method to extract absorbers and then find features of absorbers.

load_ray(new_ray)

loads a new ray into the multi_plot class.

ray_position_prop([units])

returns positional/directional properties of the ray so that it can be used like a vector

run_spice()

iteratively run the cloud method to extract all the absorbers in the lightray.

Methods Documentation

close()

close all opened files, dataset, ray

get_spectacle_absorbers()

Uses spectacle to fit a trident made spectra of the specified ion.

Returns

line_stats – Table including all line statistics found from spectacle’s fit of the spectra.

Return type

pandas.DataFrame

get_spice_absorbers(fields=[], units_dict={})

Use the SPICE method to extract absorbers and then find features of absorbers. Default outputs column density and central velocity of the absorption line (delta_v) as well as requested fields All in a pandas dataframe.

Parameters

  • fields (list, optional) – list of yt fields to extract averages of for the absorbers. Defalut: []

  • units_dict (dict, optional) – dictionary of fields and corresponding units to use for each field. Default: {}

Returns

absorber_info – Dataframe of all the absorbers and their corresponding features.

Return type

pandas.DataFrame

load_ray(new_ray)

loads a new ray into the multi_plot class. (same dataset)

Parameters

new_ray (str or yt.ray) – either filename to rayfile or a trident ray that’s already opened

ray_position_prop(units='code_length')

returns positional/directional properties of the ray so that it can be used like a vector

Parameters

units (str, optional) – YT defined units to return arrays in. defaults to ‘code length’. Default: ‘code_length’

Returns

  • ray_begin (yt.arr) – the starting coordinates of ray

  • ray_end (yt.arr) – the ending coordinates of the ray

  • ray_length (yt.arr) – the length of the ray

  • ray_unit (yt.arr) – unit vector showing direction of the ray

run_spice()

iteratively run the cloud method to extract all the absorbers in the lightray.

Returns

List of the indices that indicate the start and end of each absorber.

Return type

final_intervals: list of tuples of int