Welcome to metallicity-stack-commons’s documentation!

Metallicity_Stack_Commons

Set of common codes used in metallicity studies that use the stacking techniques

API Documentation

Metallicity_Stack_Commons package

Subpackages

analysis subpackage

Submodules

Metallicity_Stack_Commons.analysis.attenuation module

Metallicity_Stack_Commons.analysis.attenuation.Hb_SFR(log_LHb, EBV, verbose=False, log=<Logger stdout_logger (INFO)>)

Determine dust-corrected SFR using the H-beta luminosity and a measurement for nebular attenuation

Equation below is based on Eq. 2 in Ly et al. (2015), ApJ, 805, 45

DOI: https://doi.org/10.1088/0004-637X/805/1/45

Parameters

• log_LHb (Union[float, ndarray]) – Logarithm of H-beta luminosity in units of erg/s

• EBV (Union[float, ndarray]) – E(B-V) value(s)

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Union[float, ndarray]

Returns

SFRs in logarithmic units of M_sun/yr

Metallicity_Stack_Commons.analysis.attenuation.compute_A(EBV, verbose=False, log=<Logger stdout_logger (INFO)>)

Compute A(Lambda) for all possible emission lines

Parameters

• EBV (float) – E(B-V) value Has not been configured to handle a large array. Some array handling would be needed

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

dict

Returns

A(lambda) with keys identical to k_dict

Metallicity_Stack_Commons.analysis.attenuation.compute_EBV(ratio, source='HgHb', zero_neg=True, verbose=False, log=<Logger stdout_logger (INFO)>)

Determines E(B-V) from Hg/Hb or Hd/Hb flux ratios using Case B assumptions

Parameters

• ratio (Union[float, ndarray]) – Float or array containing Hg/Hb or Hd/Hb values

• source (str) – Indicate ratio type. Either ‘HgHb’ or ‘HdHb’. Default: ‘HgHb’

• zero_neg (bool) – Indicate whether to zero out negative reddening. Default: True

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Union[float, ndarray, Tuple[ndarray, ndarray]]

Returns

E(B-V) values, E(B-V) peak values

Note:

When only E(B-V) values is returned, correction does not account for negative reddening

Metallicity_Stack_Commons.analysis.attenuation.line_ratio_atten(ratio, EBV, wave_top, wave_bottom, verbose=False, log=<Logger stdout_logger (INFO)>)

Determine dust-corrected emission-line ratios

Parameters

• ratio (Union[float, ndarray]) – Float or array of observed flux ratios

• EBV (Union[float, ndarray]) – E(B-V) value(s)

• wave_top (str) – Emission-line name for flux ratio numerator

• wave_bottom (str) – Emission-line name for flux ratio denominator

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Union[float, ndarray]

Returns

Float or array of dust-corrected flux ratios

Metallicity_Stack_Commons.analysis.composite_indv_detect module

Metallicity_Stack_Commons.analysis.composite_indv_detect.main(fitspath, dataset, revised=False, det3=True, verbose=False, log=<Logger stdout_logger (INFO)>)

Reads in composite table(s) containing bin information to determine temperature-based metallicity from composite average T_e and individual line ratios ([OII]/H-beta, [OIII]/H-beta)

Parameters

• fitspath (str) – Folder full path

• dataset (str) – Sub-folder path (specific to stacking approach)

• revised (bool) – Indicates whether to use revised bin properties (e.g., revised.tbl files). Default: False

• det3 (bool) – Indicates whether individual galaxy files is limited to those satisfying emission-line det3 requirement Default: True

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Files identified by default:

composite_file: Filename of composite data

e.g., ‘[dataset]/bin_derived_properties.tbl’, ‘[dataset]/bin_derived_properties.revised.tbl’

indv_em_line_file: Filename that contains emission-line information

for each galaxy e.g., ‘individual_properties.tbl’

indv_bin_file: Filename that contains bin information for each galaxy

e.g., ‘[dataset]/individual_bin_info.tbl’

outfile: Filename of output file

e.g., ‘[dataset]/individual_derived_properties.tbl’

Metallicity_Stack_Commons.analysis.error_prop module

Metallicity_Stack_Commons.analysis.error_prop.fluxes_derived_prop(path, raw=False, binned_data=True, apply_dust=False, revised=True, verbose=False, log=<Logger stdout_logger (INFO)>)

Use measurements and their uncertainties to perform a randomization approach. The randomization is performed on individual emission lines. It carries that information to derived flux ratios and then determines electron temperature and metallicity

Parameters

• path (str) – Full path

• raw (bool) – Do a simple calculation, no randomization. Default: False

• binned_data (bool) – Whether to analyze binned data. Default: True

• apply_dust (bool) – Whether to apply dust attenuation. Default: False

• revised (bool) – Indicate if revised validation table is used. Default: True

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Metallicity_Stack_Commons.analysis.error_prop.replace_oiii4363(flux_file, detection, flux_dict, log=<Logger stdout_logger (INFO)>)

Metallicity_Stack_Commons.analysis.error_prop.write_npz(path, npz_files, dict_list, verbose=False, log=<Logger stdout_logger (INFO)>)

Write numpy files with provided dictionaries

Parameters

• path (str) – Prefix for filename output

• npz_files (list) – NPZ file names

• dict_list (list) – List of dict for each corresponding npz file

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Metallicity_Stack_Commons.analysis.fitting module

Metallicity_Stack_Commons.analysis.fitting.OIII4363_flux_limit(combine_flux_file, verbose=False, log=<Logger stdout_logger (INFO)>)

Determine 3-sigma limit on [OIII]4363 based on H-gamma measurements

Parameters

• combine_flux_file (str) – Filename of ASCII file containing emission-line flux measurements

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Optional[ndarray]

Returns

Array containing 3-sigma flux limit

Metallicity_Stack_Commons.analysis.fitting.double_gauss(x, xbar, s1, a1, c, s2, a2)

Function providing double Gaussian profile (emission and absorption) for curve_fit

Parameters

• x (ndarray) – Wavelength array

• xbar (float) – Central wavelength of Gaussian fit

• s1 (float) – Sigma (width) of first Gaussian fit (positive)

• a1 (float) – Amplitude of first Gaussian fit

• c (float) – Continuum constant for Gaussian fit

• s2 (float) – Sigma (width) of second Gaussian fit (absorption)

• a2 (float) – Amplitude of second Gaussian fit

Return type

array

Returns

Double Gaussian fit

Metallicity_Stack_Commons.analysis.fitting.gauss(x, xbar, s, a, c)

Function providing Gaussian profile for curve_fit

Parameters

• x (ndarray) – Wavelength array

• xbar (float) – Central wavelength of Gaussian fit

• s (float) – Sigma (width) of Gaussian fit

• a (float) – Amplitude of Gaussian fit

• c (float) – Continuum constant for Gaussian fit

Return type

ndarray

Returns

Gaussian fit

Metallicity_Stack_Commons.analysis.fitting.movingaverage_box1D(values, width, boundary='fill', fill_value=0.0)

Applies as boxcar kernel to smooth spectra

Parameters

• values (ndarray) – Array containing the spectrum

• width (float) – Width for smoothing

• boundary (str) – Handling of boundary values. Options are: ‘None’, ‘fill’, ‘wrap’, and ‘extend’ See astropy.convolution.convolve for more information

• fill_value (float) – Indicate fill value for default boundary=’fill’

Return type

ndarray

Returns

Array contained the smoothed/convolved spectrum

Metallicity_Stack_Commons.analysis.fitting.oxy2_gauss(x, xbar, s1, a1, c, s2, a2)

Function providing [OII] doublet Gaussian profile for curve_fit

Parameters

• x (ndarray) – Wavelength array

• xbar (float) – Central wavelength of [OII]3726 Gaussian fit

• s1 (float) – Sigma (width) of [OII]3726 Gaussian fit

• a1 (float) – Amplitude of [OII]3726 Gaussian fit

• c (float) – Continuum constant for Gaussian fit

• s2 (float) – Sigma (width) of [OII]3728 Gaussian fit

• a2 (float) – Amplitude of [OII]3728 Gaussian fit

Return type

ndarray

Returns

[OII] doublet Gaussian fit

Metallicity_Stack_Commons.analysis.fitting.rms_func(wave, dispersion, lambda_in, y0, sigma_array, mask_flag, verbose=False, log=<Logger stdout_logger (INFO)>)

Compute rms in the spectra

Parameters

• wave (ndarray) – Array of rest wavelengths

• dispersion (float) – Spectral dispersion in AA/pix

• lambda_in (float) – Central wavelength of fit

• y0 (ndarray) – Array of fluxes in units of erg/s/cm2/AA

• sigma_array (float) – Gaussian sigma (AA)

• mask_flag (ndarray) – Indicates spectra are masked for OH skyline contamination

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Returns

Metallicity_Stack_Commons.analysis.ratios module

Metallicity_Stack_Commons.analysis.ratios.flux_ratios(flux_dict, binned_data=False, get_R=True, verbose=False, log=<Logger stdout_logger (INFO)>)

Primary code to determine a variety of line ratios based on a dict containing emission-line fluxes

Parameters

• flux_dict (dict) – Contains emission-line fluxes

• get_R (bool) – Indicates populating OIII4363/OIII5007 flux ratio

• binned_data (bool) – Whether to analyze binned data. Default: False

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

dict

Returns

Emission-line flux ratios

Metallicity_Stack_Commons.analysis.temp_metallicity_calc module

Metallicity_Stack_Commons.analysis.temp_metallicity_calc.R_calculation(OIII4363, OIII5007, verbose=False, log=<Logger stdout_logger (INFO)>)

Computes the excitation flux ratio of [OIII]4363 to [OIII]5007. Adopts a 3.1-to-1 ratio for 5007/4959

Parameters

• OIII4363 (Union[float, ndarray]) – OIII4363 fluxes

• OIII5007 (Union[float, ndarray]) – OIII5007 fluxes

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Union[float, ndarray]

Returns

O++ excitation flux ratio

Metallicity_Stack_Commons.analysis.temp_metallicity_calc.metallicity_calculation(T_e, TWO_BETA, THREE_BETA, EBV=None, det3=None, verbose=False, log=<Logger stdout_logger (INFO)>)

Determines 12+log(O/H) from electron temperature and [OII]/Hb and [OIII]/Hb flux ratio

Parameters

• T_e (ndarray) – Array of electron temperatures (see temp_calculation)

• TWO_BETA (ndarray) – Array of [OII]/Hb flux ratios

• THREE_BETA (ndarray) – Array of [OIII]/Hb flux ratios

• EBV (Optional[ndarray]) – Optional array containing EBV distribution

• det3 (Optional[ndarray]) –

  Optional array to pass in to identify those satisfying det3 requirements. Default: None means full array is considered

  Note: for Monte Carlo inputs, a 1-D np.array index satisfying

  det3 requirements will suffice

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

dict

Returns

Contains 12+log(O/H), O+/H, O++/H, log(O+/H), log(O++/H)

Metallicity_Stack_Commons.analysis.temp_metallicity_calc.temp_calculation(R, EBV=None, verbose=False, log=<Logger stdout_logger (INFO)>)

Computes electron temperature (T_e) from O++ excitation flux ratio

Formula is:

T_e = a(-log(R)-b)^(-c) where a = 13025, b=0.92506, and c=0.98062 (Nicholls et al. 2014)

Parameters

• R (ndarray) – Array of O++ excitation flux ratio (see R_calculation)

• EBV (Optional[ndarray]) – Array of E(B-V). Set to zero if not applying attenuation

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

ndarray

Returns

Array of T_e (Kelvins)

Module contents

others subpackage

Submodules

Metallicity_Stack_Commons.others.extract_deep2_data module

Metallicity_Stack_Commons.others.extract_deep2_data.main(infile, log=<Logger stdout_logger (INFO)>)

Import previous DEEP2 Ly et al. (2015) dataset and export an astropy Table called bin_fit.tbl

Parameters

• infile (str) – Input filename

• log (Logger) – logging.Logger object

Module contents

plotting subpackage

Submodules

Metallicity_Stack_Commons.plotting.balmer module

balmer

Generates plots illustrating Balmer recombination lines

This code was created from:

https://github.com/astrochun/Zcalbase_gal/blob/master/Analysis/DEEP2_R23_O32/balmer_plots.py

Metallicity_Stack_Commons.plotting.balmer.HbHgHd_fits(fitspath, out_pdf_prefix='HbHgHd_fits', use_revised=False, verbose=False, log=<Logger stdout_logger (INFO)>)

Generate PDF plots that illustrate H-delta, H-gamma, and H-beta line profiles and best fit

Parameters

• fitspath (str) – Full path

• out_pdf_prefix (str) – Prefix for output PDF file

• use_revised (bool) – Indicate whether to use regular or revised tables

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Metallicity_Stack_Commons.plotting.balmer.extract_fit(astropy_table, line_name, balmer=False, verbose=False, log=<Logger stdout_logger (INFO)>)

Extract best fit from table and fluxes, return a list of fitting parameters and fluxes

Parameters

• astropy_table (Table) – Astropy table containing fitting result

• line_name (str) – Name of Line to extract fit results

• balmer (bool) – Indicate whether line is a Balmer line

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Optional[dict]

Returns

Fitting results

Metallicity_Stack_Commons.plotting.balmer.fitting_result(wave, y_norm, lambda_cen, line_fit, line_fit_neg, flux_gauss, flux_spec, use_revised=False)

Returns fitting results based on inputs of best fit

Parameters

• wave (ndarray) – Array of rest-frame wavelengths

• y_norm (ndarray) – Normalize 1-D spectra in units of 10^-17 erg/s/cm2/AA

• lambda_cen (float) – Central wavelength in Angstroms

• line_fit (list) – List containing Balmer emission fits

• line_fit_neg (list) – List containing the absorption (“stellar”) Balmer fit

• flux_gauss (float) – Flux from Gaussian model

• flux_spec (float) – Flux from spectrum (above median)

• use_revised (bool) – Indicate whether fluxes have been revised. Default: False

Return type

dict

Returns

Dictionary of fitting results

Module contents

Submodules

Metallicity_Stack_Commons.column_names module

Metallicity_Stack_Commons.column_names.indv_M_LHb()

Use remove_from_list() to provide simplified list that contains ID, logM and logLHb

Return type

list

Returns

List containing just ID, logM, logLHb

Metallicity_Stack_Commons.column_names.indv_R23_O32()

Use remove_from_list() to provide simplified list that contains ID, logR23 and logO32

Return type

list

Returns

List containing just ID, logR23, logO32

Metallicity_Stack_Commons.column_names.line_fit_suffix_add(line_name0, line_type0)

Simple list comprehension combining emission line fit suffixes with the emission line. This works for individual lines

Parameters

• line_name0 (str) – Line name

• line_type0 (str) – Emission-line type (e.g., ‘Balmer’)

Return type

list

Returns

List of strings formatted as [LINE]_[SUFFIX]

Metallicity_Stack_Commons.column_names.merge_column_names(*args)

Merges multiple lists containing column names.

Usage:

column_names = merge_column_names(bin_names0, indv_names0)

Parameters

args (list) – An undefined number of lists

Return type

list

Returns

Merged list

Metallicity_Stack_Commons.column_names.remove_from_list(list0, remove_entries)

Purpose:

Remove entries from list of column names

Parameters

• list0 (list) – List of column names

• remove_entries (list) – List of column names to remove

Return type

list

Returns

List of column names after removal

Metallicity_Stack_Commons.logging module

class Metallicity_Stack_Commons.logging.LogClass(log_dir, logfile)

Bases: object

Main class to log information to stdout and ASCII logfile

Note: This code is identical to the one used in ReQUIAM:

https://github.com/ualibraries/ReQUIAM

To use:

log = LogClass(log_dir, logfile).get_logger()

Parameters

• log_dir (str) – Relative path for exported logfile directory

• logfile (str) – Filename for exported log file

get_logger()

Return type

Logger

Metallicity_Stack_Commons.logging.get_user_hostname()

Retrieve user, hostname, IP, and OS configuration

Return type

dict

Returns

Dictionary with ‘user’ ‘hostname’ and ‘ip’ keys

Metallicity_Stack_Commons.logging.log_stdout()

Returns stdout logging object

Return type

Logger

Metallicity_Stack_Commons.logging.log_verbose(log, message, verbose=False)

Log message depending on verbosity

Parameters

• log (Logger) – logging.Logger object

• message (str) – Message

• verbose (bool) – Write verbose message to stdout. Default: file only

Metallicity_Stack_Commons.update_det4363_info module

Metallicity_Stack_Commons.update_det4363_info.get_index(det4363_table, input_table, column_name, verbose=False, log=<Logger stdout_logger (INFO)>)

Uses either OBJNO or AP/SLIT info to get index for an existing table

Parameters

• det4363_table (Table) – Astropy table containing DEEP2 [OIII]4363-detected sample

• input_table (Table) – Astropy table containing the entire sample to be updated

• column_name (str) – Column name for cross-matching

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

Tuple[ndarray, ndarray]

Returns

Index arrays for det4363_table, input_table

Metallicity_Stack_Commons.valid_table module

Metallicity_Stack_Commons.valid_table.compare_to_by_eye(fitspath, dataset)

This function takes the automated validation table and checks it against inputted measurement that are determined by eye. These inputted measurements are in the np.where statements. It outputs a revised validation table based on the inputted measurements.

Usage:

valid_table.make_validation_table(fitspath, dataset)

Parameters

• fitspath (str) – Full file path where the input file is and where the output file will be placed.

• dataset (str) – Determine which eye measurements to use

Outputs:

fitspath + ‘bin_validation_revised.tbl’ and ‘.csv’

Validation table containing bin IDs; number of galaxies in each bin; and column indicating OIII4363 detection/non-detection, OIII4363_Flux_Observed, OIII4363_S/N, Notes

Metallicity_Stack_Commons.valid_table.make_validation_table(fitspath, vmin_4363SN=3, vmin_5007SN=100, vmax_4363sig=1.6, rlmin_4363SN=3, rlmax_4363sig=1.6, rlmin_5007SN=100)

This function creates a validation table for a given binning set. The validation table contains a OIII4363 detection column where 1.0 means detection, 0.5 means non-detection with reliable OIII5007, and 0.0 means unreliable non-detection. This function will be run every time the analysis is completed and will create a validation table for every analysis.

Usage:

valid_table.make_validation_table(fitspath, bin_type_str)

Parameters

• fitspath (str) – Full file path where the input file is and where the output file will be placed.

• vmin_4363SN – int. minimum OIII4363 S/N for valid detection

• vmin_5007SN – int. minimum OIII5007 S/N for valid detection

• vmax_4363sig – int. maximum OIII4363 sigma for valid detection

• rlmin_4363SN – int. minimum OIII4363 S/N for robust limit

• rlmax_4363sig – int. maximum OIII4363 sigma for robust limit

• rlmin_5007SN – int. minimum OIII5007 S/N for robust limit

Outputs:

fitspath + ‘bin_validation.tbl’

Validation table containing bin IDs; number of galaxies in each bin; and column indicating OIII4363 detection/non-detection, OIII4363_Flux_Observed, OIII4363_S/N

Common functions

Metallicity_Stack_Commons.dir_date(folder_name, path_init='', year=False, verbose=False, log=<Logger stdout_logger (INFO)>)

This function finds and returns the path to a directory named after the current date (MMDDYYYY). If the directory doesn’t exist yet, it creates a new directory named after the current date in the provided folder_name directory.

Originally from https://github.com/rafia37/Evolution-of-Galaxies/blob/master/general.py

Usage:

fitspath = dir_date(folder_name, year=True)

Parameters

• folder_name (str) – Directory for date subdirectory will be in

• path_init (str) – root path. Default: empty string

• year (bool) – Indicate whether to include year in date folder. Default: False

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

str

Returns

Full path to the date directory

Metallicity_Stack_Commons.exclude_outliers(objno, verbose=False, log=<Logger stdout_logger (INFO)>)

Exclude spectra that are identified as outliers.

Generally this is because the spectra have very high S/N on the continuum.

Parameters

• objno (Union[list, ndarray]) – Array of eight-digit identifier

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

ndarray

Returns

Array of zeros (not flagged) and ones (flagged

Metallicity_Stack_Commons.get_user(username=None, verbose=False, log=<Logger stdout_logger (INFO)>)

Get the corresponding path for a given username

Parameters

• username (Optional[str]) – Optional input for username

• verbose (bool) – Write verbose message to stdout. Default: file only

• log (Logger) – logging.Logger object

Return type

str

Returns

Full path to the date directory

Indices and tables

• Index

• Module Index

• Search Page