LineList

class msaexp.utils.LineList(data=None)

Bases: object

Tools for working with a table of lines

Examples

from msaexp.utils import LineList

ll = LineList()
fig = ll.demo()

(Source code, png, hires.png, pdf)

Attributes Summary

CLEAN_CENTER_KWARGS
LEFT_OFFSET_KWARGS
N
RIGHT_OFFSET_KWARGS
WHITE_BBOX

Methods Summary

add_to_axis(ax[, wave_pixels, bottom, top, ...])	Add vlines and labels to axis
append_scaled_orders([priorities, orders, ...])	Add rows to the data table for higher spectral orders where wavelength multiplied by $m=2,3,...$
demo([xlim, figsize])	Show a demonstration of various plot options
from_table(tab[, wave_column, to_angstroms, ...])	Generate from normal table with a list of line wavelengths
insert_spaces_in_labels()	Insert extra spaces in ion names
load_data([fill_color])	Load the data from msaexp/data/linelist.ecsv
select_lines([z, wave_range, prefixes, ...])	Get selection of lines within a wavelength range
spec_model(spec[, z, selected, fnu, use_ratios])	Make line models msaexp.spectrum.SpectrumSampler.fast_emission_line

Attributes Documentation

CLEAN_CENTER_KWARGS = {'bbox': {'alpha': 1.0, 'boxstyle': 'square,pad=0.3', 'ec': 'None', 'fc': 'w'}, 'ha': 'center', 'x_pad': 0.0}

LEFT_OFFSET_KWARGS = {'ha': 'right', 'x_pad': -0.005}

N

RIGHT_OFFSET_KWARGS = {'ha': 'left', 'x_pad': 0.005}

WHITE_BBOX = {'alpha': 1.0, 'boxstyle': 'square,pad=0.3', 'ec': 'None', 'fc': 'w'}

Methods Documentation

add_to_axis(ax, wave_pixels=None, bottom=0, top=1.0, x_pad=0, wfunc=<function min>, y_label=0.98, priorities=[3, 4, 5], label_priorities=None, label_prefixes=[], y_normalized=True, rotation=90, ha='center', va='top', lw=1.5, ls='-', fontsize=7, alpha=0.8, label_alpha=None, bbox={'alpha': 1.0, 'boxstyle': 'square,pad=0.3', 'ec': 'None', 'fc': 'w'}, zorder=1, label_zorder=None, **kwargs)

Add vlines and labels to axis

Parameters

axmatplotlib axis

Axis to draw labels in

bottomfloat, (array-like, array-like)

Lower limit of vlines to draw. If two arrays are provided, will interpolate the value value = np.interp(wave, *bottom)

topfloat, (array-like, array-like)

Upper limit of the vlines, with same interpolation options as bottom

x_padfloat

relative padding for text labels

wfuncfunc

Function to apply to the potential multiple entries for line complexes to specify where to draw the labels

y_labelfloat

Vertical location of the line text labels

prioritieslist

List of priorities to include from the linelist table

label_prioritieslist, None

List of priorities to include with text labels. If not provided, will be the same as priorities

label_prefixeslist

Prefix filtering for lines with text labels

y_normalizedbool

If True, the bottom, top and y_label values are calculated in the normalized frame of the plot extent, i.e., with 0 at the bottom and 1 at the top. Not used if values are interpolated.

lw, lsfloat, string

Linewidth and linestyle properties for the vlines

rotation, ha, va, fontsize, alpha, bbox, zorder

Text label properties

Returns

datatable

View of the linelist table with the selected lines

append_scaled_orders(priorities=[5], orders=[2, 3], priority_offset=100, append=True)

Add rows to the data table for higher spectral orders where wavelength multiplied by $m=2,3,…$

Parameters

prioritieslist, None

List of priorities to include

orderslist

List of order integers

priority_offsetfloat

New rows will have priority + priority_offset

appendbool

Append new rows directly to the data attribute table

Returns

order_rowstable

Table with wavelengths scaled by the requested orders and updated labels

demo(xlim=[0.35, 0.51], figsize=(8, 8))

Show a demonstration of various plot options

static from_table(tab, wave_column='wavelength', to_angstroms=1.0, color='0.5', priority=5, prefix='', ratio_column=None)

Generate from normal table with a list of line wavelengths

insert_spaces_in_labels()

Insert extra spaces in ion names

load_data(fill_color='0.2')

Load the data from msaexp/data/linelist.ecsv

select_lines(z=0, wave_range=[0, inf], prefixes=[], exclude_prefixes=[], priorities=[4, 5], floor=True, max_microns=500, **kwargs)

Get selection of lines within a wavelength range

Parameters

zfloat

Redshift

wave_range[float, float]

Observed-frame wavelength range. The script tries to automatically distinguish between wavelength units of Angstroms or microns assuming the latter if wave_range[1] < 500

prefixeslist

List of strings compared to the name column in the linelist using the test name.startswith(prefix)

prioritieslist

List of linelist priorities to include

floorbool

If true, ignore decimal part of the linelist priorities and just compare the integer values

max_micronsfloat

Threshold compared to max(x) above which wavelengths are interpreted to be $mathrm{AA}$ rather than $mumathrm{m}$

Returns

——-

selectedboolean array

Selection array on the listlist table that satisfy the selection criteria

x_scalefloat

Scale factor needed to put the “wavelength” column of the linelist in the frame of wave_range

spec_model(spec, z=0, selected=None, fnu=True, use_ratios=True, **kwargs)

Make line models msaexp.spectrum.SpectrumSampler.fast_emission_line

Parameters

specSpectrumSampler

Spectrum object

zfloat

Redshift

selectedNone, array

Line selection array. If not provided, will pull from LineList.select_lines.

fnubool

Return in fnu units

use_ratiosbool

Use line ratio values. If False, normalize line flux to unity.

kwargsdict

Keyword arguments passed to LineList.select_lines and msaexp.spectrum.SpectrumSampler.fast_emission_line

Returns

resultdict

Model results:

• templates: (Nline, Nwave) array. of line templates

• names: line names

• index: indices of the selected lines from the full linelist