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set_parameters.m
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set_parameters.m
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% set_parameters: sets various parameters for the DLA detection
% pipeline
% physical constants
lya_wavelength = 1215.6701; % Lyman alpha transition wavelength Å
lyb_wavelength = 1025.7223; % Lyman beta transition wavelength Å
lyman_limit = 911.7633; % Lyman limit wavelength Å
speed_of_light = 299792458; % speed of light m s⁻¹
% converts relative velocity in km s^-1 to redshift difference
kms_to_z = @(kms) (kms * 1000) / speed_of_light;
% utility functions for redshifting
emitted_wavelengths = ...
@(observed_wavelengths, z) (observed_wavelengths / (1 + z));
observed_wavelengths = ...
@(emitted_wavelengths, z) ( emitted_wavelengths * (1 + z));
% file loading parameters
loading_min_lambda = 910; % range of rest wavelengths to load Å
loading_max_lambda = 1217;
% preprocessing parameters
z_qso_cut = 2.15; % filter out QSOs with z less than this threshold
min_num_pixels = 200; % minimum number of non-masked pixels
% normalization parameters
normalization_min_lambda = 1310; % range of rest wavelengths to use Å
normalization_max_lambda = 1325; % for flux normalization
% null model parameters
min_lambda = 911.75; % range of rest wavelengths to Å
max_lambda = 1215.75; % model
dlambda = 0.25; % separation of wavelength grid Å
k = 20; % rank of non-diagonal contribution
max_noise_variance = 1^2; % maximum pixel noise allowed during model training
% optimization parameters
initial_c_0 = 0.1; % initial guess for c₀
initial_tau_0 = 0.0023; % initial guess for τ₀
initial_beta = 3.65; % initial guess for β
minFunc_options = ... % optimization options for model fitting
struct('MaxIter', 2000, ...
'MaxFunEvals', 4000);
% DLA model parameters: parameter samples
num_dla_samples = 10000; % number of parameter samples
alpha = 0.9; % weight of KDE component in mixture
uniform_min_log_nhi = 20.0; % range of column density samples [cm⁻²]
uniform_max_log_nhi = 23.0; % from uniform distribution
fit_min_log_nhi = 20.0; % range of column density samples [cm⁻²]
fit_max_log_nhi = 22.0; % from fit to log PDF
% model prior parameters
prior_z_qso_increase = kms_to_z(30000); % use QSOs with z < (z_QSO + x) for prior
% instrumental broadening parameters
width = 3; % width of Gaussian broadening (# pixels)
pixel_spacing = 1e-4; % wavelength spacing of pixels in dex
% DLA model parameters: absorber range and model
num_lines = 3; % number of members of the Lyman series to use
max_z_cut = kms_to_z(3000); % max z_DLA = z_QSO - max_z_cut
max_z_dla = @(wavelengths, z_qso) ... % determines maximum z_DLA to search
(max(wavelengths) / lya_wavelength - 1) - max_z_cut;
min_z_cut = kms_to_z(3000); % min z_DLA = z_Ly∞ + min_z_cut
min_z_dla = @(wavelengths, z_qso) ... % determines minimum z_DLA to search
max(min(wavelengths) / lya_wavelength - 1, ...
observed_wavelengths(lyman_limit, z_qso) / lya_wavelength - 1 + ...
min_z_cut);
% base directory for all data
base_directory = 'data';
% utility functions for identifying various directories
distfiles_directory = @(release) ...
sprintf('%s/%s/distfiles', base_directory, release);
spectra_directory = @(release) ...
sprintf('%s/%s/spectra', base_directory, release);
processed_directory = @(release) ...
sprintf('%s/%s/processed', base_directory, release);
dla_catalog_directory = @(name) ...
sprintf('%s/dla_catalogs/%s/processed', base_directory, name);
% replace with @(varargin) (fprintf(varargin{:})) to show debug statements
fprintf_debug = @(varargin) ([]);