GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final module

Telluric removal module using PCA (Principal Component Analysis) in the wavelength domain. This module processes spectroscopic data to remove telluric features using PCA decomposition.

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.combine(path_night_completef, name, transpose_read, repeatf=None, sort_indices=None)

Combine A and B channel data into a single dataset.

Parameters:

• path_night_completef – Path to the night’s data

• name – Base name for the files

• transpose_read – Whether to transpose the data during reading

• repeatf – Optional file name for repeating dimensions

• sort_indices – Optional indices to sort the combined data (if None, interleave A and B)

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.combine_nfc(path_night_completef)

Copy A_nfc.fits to nfc.fits.

Parameters:

path_night_completef – Path to the night’s data

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.load_fase_data(file_path)

Load phase data from file, handling both dictionary and legacy formats.

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.combine_fase(path_night_completef)

Combine phase data from A and B channels into a single file.

Handles both new dictionary format and legacy sequential format for backward compatibility.

Parameters:

path_night_completef – Path to the night directory

Returns:

Indices used to sort the combined data based on hjd

Return type:

sort_indices

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.combine_maskinv_err_pca(path_night_completef)

Combine mask_good and error information from A and B channels.

Parameters:

path_night_completef – Path to the night’s data

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.median_idl(arr)

Calculate median using IDL-like tell_rm_method.

Parameters:

arr – Input array

Returns:

Median value

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.linear_solver(topca_l, res_l)

Solve linear system using SVD decomposition.

Parameters:

• topca_l – Input data matrix

• res_l – Result matrix

Returns:

Reconstructed array

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.plot_tangent(pdf_tangentf, current_order, tan_sncf, der_secf, tangent_thresholdf, n_components_pcaf)

Plot tangent information for PCA component selection.

Parameters:

• pdf_tangentf – PDF file to save plot

• current_order – Order

• tan_sncf – Tangent signal-to-noise curve

• der_secf – Second derivative

• tangent_thresholdf – Threshold for tangent

• n_components_pcaf – Number of PCA components

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.plot_process(initial_spectrum, spectrum_after_mask, log_spectrum_after_mask, log_normalized_spectrum_after_mask, log_residuals_after_reconstruction, log_residuals_after_reconstruction_and_eventual_smooth, wl_order, pdf_processf, n_pixels, oi, phases)

Plot processing steps for telluric removal.

Parameters:

• initial_spectrum – Initial data

• spectrum_after_mask – Data after masking

• log_spectrum_after_mask – Logarithmic of data after masking

• log_normalized_spectrum_after_mask – Logarithmic of normalized data after masking

• log_residuals_after_reconstruction – Residuals after reconstruction

• log_residuals_after_reconstruction_and_eventual_smooth – Residuals after reconstruction and eventual smoothing

• wl_order – Wavelength array for order

• pdf_processf – PDF file to save plots

• n_pixels – Number of pixels

• oi – Order index

• phases – Planetary orbital phases

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.plot_process2(initial_spectrum, log_spectrum_after_mask, log_residuals_after_reconstruction, array_reconstructed_from_PCA_components, wl_order, pdf_processf, n_pixels, oi, phases)

Plot processing steps for telluric removal.

Parameters:

• initial_spectrum – Initial data

• log_spectrum_after_mask – Logarithmic of data after masking

• log_residuals_after_reconstruction – Residuals after reconstruction

• array_reconstructed_from_PCA_components – array reconstructed from PCA components

• wl_order – Wavelength array for order

• pdf_processf – PDF file to save plots

• n_pixels – Number of pixels

• oi – Order index

• phases – Planetary orbital phases

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.plot_order(current_order, x_arrf, maskf, resf, pdff)

Plot order information.

Parameters:

• current_order – Order index

• x_arrf – X-axis array

• maskf – Mask array

• resf – Result array

• pdff – PDF file to save plot

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.plot_mean_sp(current_order, meanspf, normmeansp, continuumf, sigma_coefff, maskinv1f, maskinv2f, cutofff, threshold_mean, pdf_mean_spf, wlen)

Plot mean spectrum with masks.

Parameters:

• current_order – Order

• meanspf – Mean spectrum

• normmeansp – Normalized Mean spectrum

• continuumf – Continuum

• sigma_coefff – Sigma coefficient for variance-based masking

• maskinv1f – First mask inverse (cutoff + threshold)

• maskinv2f – Second mask inverse (sigma-based)

• cutofff – Cutoff value for telluric masking

• threshold_mean – Threshold for mean spectrum masking

• pdf_mean_spf – PDF file to save plot

• wlen – Wavelength array for order

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.divide_by_brightest(spectra_order, n_images, n_brightest=50)

Normalize spectra by dividing each exposure by the median of its brightest pixels.

Parameters:

• spectra_order – 2D array of spectral data (pixels x images)

• n_images – Number of images (exposures)

• n_brightest – Number of brightest pixels to use for normalization

Returns:

(spectra_order, spectra_order_before_mask) - cleaned input and normalized spectra

Return type:

tuple

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.masking_function(masking, spectra_order_before_mask, cutoff, threshold_mean_spec, sigma_coeff, checkbox_save_plot, good_order_oi, pdf_mean_sp, n_pixels, do_not_fit_continuum, wlen)

Apply spectral masking based on telluric absorption and variance criteria.

Parameters:

• masking – Whether to apply masking

• spectra_order_before_mask – Normalized spectral data (pixels x images)

• cutoff – Cutoff threshold for telluric line detection

• threshold_mean_spec – Threshold for mean spectrum signal level

• sigma_coeff – Coefficient for variance-based masking

• checkbox_save_plot – Whether to save diagnostic plots

• good_order_oi – Order index for plot labeling

• pdf_mean_sp – PDF file for saving mean spectrum plots

• n_pixels – Number of spectral pixels

• do_not_fit_continuum – Whether to skip continuum fitting

• wlen – Wavelength array for order

Returns:

(std_after_full_norm, spectra_order_after_mask, mask_inv,

count_mask_inv, mask_good, amount_good_pixels)

Return type:

tuple

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.tangent_method_for_PCA(pca_obj, log_spectra_order_after_mask, max_n_components_per_order, spectra_order_after_mask, result_first_pca, mask_good, epsilon, tangent_threshold, substitute_for_comp, current_order, checkbox_save_plot, pdf_tangent, pca_mode)

Determine optimal number of PCA components using the tangent method.

Analyzes the variance reduction curve to find where adding more PCA components provides diminishing returns, using derivatives of the standard deviation.

Parameters:

• pca_obj – Fitted PCA object with explained_variance_ attribute

• log_spectra_order_after_mask – Log-transformed masked spectral data

• max_n_components_per_order – Range of component numbers to test

• spectra_order_after_mask – Masked spectral data (used for shape)

• result_first_pca – PCA components from initial fit

• mask_good – Indices of good (unmasked) pixels

• epsilon – Small value to avoid division by zero

• tangent_threshold – Threshold for second derivative test

• substitute_for_comp – Fallback number of components

• current_order – Current order index for logging

• checkbox_save_plot – Whether to save tangent diagnostic plot

• pdf_tangent – PDF file for saving tangent plot

• pca_mode – PCA decomposition mode (‘spatial’ or ‘temporal’)

Returns:

Optimal number of PCA components

Return type:

int

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.cross_val_score_components(pca_obj, pca_scores, max_n_components_per_order, log_spectra_order_after_mask)

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.get_number_of_components_PCA(auto_components, log_spectra_order_after_mask, max_n_components_per_order, spectra_order_after_mask, mask_good, epsilon, tangent_threshold, substitute_for_comp, current_order, checkbox_save_plot, pdf_tangent, entry_min_comp, entry_max_comp, entry_fixed_comp, tangent_method, apply_standardize, pca_mode)

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.apply_smooth(log_final_pca, smooth_size, mask_good)

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.tell_rem_wl_log2(exchange_pathf)

Main function for telluric removal using PCA with wavelength calibration.

Parameters:

exchange_pathf – Path to exchange directory containing parameters

GUIBRUSHR.GUI.Input_Output_Panels.Input_Panels.TabPanels.FrameTellRem.tell_rem_pca_wl_log_final.main()

Main function for telluric removal using PCA in wavelength domain.

Command line usage:

python tell_rem_pca_wl_log_final.py <exchange_path> <path_default>

Args (from command line):

exchange_path: Path to exchange directory with input data path_default: Default path for GUIBRUSHR modules