Functions
cpl_polynomial *	eris_ifu_lcorr_get (cpl_imagelist cube, hdrl_imagelist hdrlCube, const cpl_propertylist header, cpl_vector peaks, const int pfit_order)
	Create wavelength correction polynomial from IFU cube using OH lines.

cpl_bivector *	eris_ifu_lcorr_extract_spectrum (const cpl_imagelist cube, const cpl_propertylist header, const double min_frac, const cpl_vector *range)
	Extract integrated spectrum from IFU cube for brightest spaxels.

cpl_image *	eris_ifu_lcorr_create_object_mask (const cpl_imagelist cube, double min_frac, const cpl_vector lambda, const cpl_vector *range)
	Create spaxel selection mask for spectrum extraction.

cpl_vector *	eris_ifu_lcorr_create_lambda_vector (const cpl_propertylist *header)
	Create wavelength vector from FITS header WCS keywords.

cpl_bivector *	eris_ifu_lcorr_read_OH_reference_spectrum (const char *filename, cpl_size ext_number)
	Read OH reference spectrum from FITS file.

cpl_array *	eris_ifu_lcorr_get_peak_positions (const cpl_bivector spectrum, double min_frac, cpl_vector range)
	Detect emission line peak positions in a spectrum.

cpl_vector *	eris_ifu_lcorr_get_peak_lambdas (const cpl_bivector spectrum, double min_frac, cpl_vector range)
	Detect and refine emission line peak wavelengths using Gaussian fitting.

int	gauss1d_fnc (const double x[], const double a[], double *result)
	define a Gaussian profile

int	gauss1d_fncd (const double x[], const double a[], double result[])
	define a Gaussian profile

double	fit_peak (const cpl_bivector spectrum, const cpl_size size, double lambda_in, int half_width, double sigma_par)
	fit a peak

cpl_polynomial *	eris_ifu_lcorr_crosscorrelate_spectra (cpl_bivector object, cpl_vector peaks, ifsBand bandId, const int pfit_order)
	cross-correlate two input spectra

void	eris_ifu_lcorr_open_debug_file (const char *filename)
	open ASCII file to hold debug results

void	eris_ifu_lcorr_close_debug_file (void)
	close ASCII file that hold debug results

Detailed Description

This module provides functions for wavelength (lambda) correction of IFU spectra using OH sky line emission features. The correction compensates for flexure-induced wavelength shifts by cross-correlating observed OH lines with reference positions.

The typical workflow is:

Extract an integrated spectrum from the IFU cube
Detect OH emission line peaks in the extracted spectrum
Cross-correlate observed peaks with reference OH line positions
Fit a polynomial correction that maps observed wavelengths to true wavelengths
Apply the correction to the entire wavelength solution

The correction polynomial can be of varying degree (typically 0-3), with higher degrees allowing for non-linear wavelength distortions but requiring more detected lines.

Function Documentation

◆ eris_ifu_lcorr_close_debug_file()

void eris_ifu_lcorr_close_debug_file ( void )

close ASCII file that hold debug results

Definition at line 1433 of file eris_ifu_lambda_corr.c.

◆ eris_ifu_lcorr_create_lambda_vector()

cpl_vector * eris_ifu_lcorr_create_lambda_vector ( const cpl_propertylist * header )

Create wavelength vector from FITS header WCS keywords.

Constructs a wavelength vector using the WCS (World Coordinate System) properties of the spectral axis (axis 3) from a data cube's FITS header. Uses the standard FITS keywords NAXIS3, CRVAL3, CDELT3, and CRPIX3.

Parameters

header Property list (FITS header) containing WCS keywords

Returns: Vector of wavelengths in microns, or NULL on error

Note: The returned vector must be deallocated with cpl_vector_delete(); Required FITS keywords: NAXIS3, CRVAL3, CDELT3, CRPIX3; Wavelength for plane i is: lambda[i] = (i+1 - CRPIX3) * CDELT3 + CRVAL3

Definition at line 436 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_NULL, CATCH, CATCH_MSG, and TRY.

Referenced by eris_ifu_dar_correction(), eris_ifu_lcorr_extract_spectrum(), and eris_ifu_sky_tweak().

◆ eris_ifu_lcorr_create_object_mask()

cpl_image * eris_ifu_lcorr_create_object_mask	(	const cpl_imagelist *	cube,
		double	min_frac,
		const cpl_vector *	lambda,
		const cpl_vector *	range
	)

Create spaxel selection mask for spectrum extraction.

For every spaxel, calculates median flux (optionally restricted to specific wavelength ranges) and creates a binary mask selecting the brightest fraction of spaxels. This mask is used to extract an integrated spectrum from the brightest regions of the field.

Parameters

cube	Input data cube (imagelist)
min_frac	Fraction of brightest spaxels to select (0.0-1.0, e.g., 0.8 for top 80%)
lambda	Wavelength vector corresponding to cube's spectral axis, or NULL
range	Wavelength ranges for flux calculation (NULL for all wavelengths) Format: [min1, max1, min2, max2, ...] pairs in microns

Returns: Binary mask image (1.0=selected, 0.0=rejected), or NULL on error

Note: Either both lambda and range must be provided, or both must be NULL; The range vector must have an even number of elements (lower/upper pairs); Each lambda entry corresponds to one plane in the cube's z-axis; The returned image must be deallocated with cpl_image_delete(); When range is specified, only wavelengths within the specified range(s) contribute to the median flux calculation for spaxel selection

Definition at line 283 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, CATCH, CATCH_MSG, eris_ifu_mask_nans_in_cube(), and TRY.

Referenced by eris_ifu_lcorr_extract_spectrum(), eris_ifu_plot_cube_background(), and eris_ifu_sky_tweak().

◆ eris_ifu_lcorr_crosscorrelate_spectra()

cpl_polynomial * eris_ifu_lcorr_crosscorrelate_spectra	(	cpl_bivector *	object,
		cpl_vector *	peaks,
		ifsBand	bandId,
		const int	pfit_order
	)

cross-correlate two input spectra

Parameters

object	input spectrum
peaks	peaks
bandId	band setup
pfit_order

Returns: polynomial with solution in case of success, NULL otherwise.

Definition at line 1139 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, CATCH, CATCH_MSG, CHECK_ERROR_STATE, eris_ifu_get_band_resolution(), fit_peak(), and TRY.

Referenced by eris_ifu_lcorr_get().

◆ eris_ifu_lcorr_extract_spectrum()

cpl_bivector * eris_ifu_lcorr_extract_spectrum	(	const cpl_imagelist *	cube,
		const cpl_propertylist *	header,
		const double	min_frac,
		const cpl_vector *	range
	)

Extract integrated spectrum from IFU cube for brightest spaxels.

Creates an integrated spectrum by selecting the brightest spaxels in the cube (based on median flux) and summing their spectral contributions. This produces a high signal-to-noise spectrum suitable for OH line detection and wavelength calibration.

Parameters

cube	Input data cube (imagelist with spectral axis)
header	FITS header containing WCS keywords (NAXIS3, CRVAL3, CDELT3, CRPIX3)
min_frac	Fraction of brightest spaxels to include (e.g., 0.8 = brightest 80%)
range	Optional wavelength ranges to consider for spaxel selection (NULL for all) Format: [min1, max1, min2, max2, ...] in microns

Returns: Bivector with X=wavelengths (microns) and Y=integrated flux, or NULL on error

Note: The returned bivector must be deallocated with cpl_bivector_delete(); Spaxel selection is based on median flux across the specified wavelength range(s); The wavelength vector is computed from WCS keywords in the header

Definition at line 213 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, CATCH, CATCH_MSG, eris_ifu_extract_spec(), eris_ifu_lcorr_create_lambda_vector(), eris_ifu_lcorr_create_object_mask(), and TRY.

Referenced by eris_ifu_lcorr_get().

◆ eris_ifu_lcorr_get()

cpl_polynomial * eris_ifu_lcorr_get	(	cpl_imagelist *	cube,
		hdrl_imagelist *	hdrlCube,
		const cpl_propertylist *	header,
		cpl_vector *	peaks,
		const int	pfit_order
	)

Create wavelength correction polynomial from IFU cube using OH lines.

This is the main entry point for lambda correction. It extracts an integrated spectrum from the input cube, detects OH emission line peaks, and cross-correlates them with reference line positions to derive a wavelength correction polynomial.

Parameters

cube	Input data cube (CPL imagelist format), set to NULL if hdrlCube is provided
hdrlCube	Input data cube (HDRL imagelist format), set to NULL if cube is provided
header	FITS header containing WCS and instrument information
peaks	Vector containing reference OH line wavelengths (in microns)
pfit_order	Order of polynomial fit (0=constant shift, 1=linear, 2=quadratic, etc.)

Returns: Polynomial representing the wavelength correction, or NULL on error

Note: Exactly one of cube or hdrlCube must be non-NULL; The returned polynomial must be deallocated with cpl_polynomial_delete(); The correction polynomial maps observed wavelengths to corrected wavelengths: lambda_corrected = lambda_observed + polynomial(lambda_observed); A polynomial order of 0 is recommended for K-band to avoid extrapolation errors; Higher orders (1-3) may improve accuracy in H and J bands with many detected lines

Definition at line 84 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, CATCH, CHECK_ERROR_STATE, eris_ifu_get_band(), eris_ifu_lcorr_crosscorrelate_spectra(), eris_ifu_lcorr_extract_spectrum(), eris_ifu_mask_nans_in_cube(), hdrl_image_get_image(), hdrl_imagelist_get(), hdrl_imagelist_get_size(), and TRY.

Referenced by eris_ifu_jitter_process_exposures().

◆ eris_ifu_lcorr_get_peak_lambdas()

cpl_vector * eris_ifu_lcorr_get_peak_lambdas	(	const cpl_bivector *	spectrum,
		double	min_frac,
		cpl_vector *	range
	)

Detect and refine emission line peak wavelengths using Gaussian fitting.

Identifies emission line peaks in the input spectrum and refines their positions by fitting Gaussian profiles. Outlier peaks are rejected based on statistical analysis of fitted wavelength shifts and line widths (sigma). This produces a clean set of well-measured line wavelengths suitable for wavelength calibration.

Parameters

spectrum	Input spectrum as bivector (X=wavelength in microns, Y=flux)
min_frac	Minimum flux threshold as fraction of maximum flux (0.0-1.0)
range	Optional wavelength ranges to search (NULL for all wavelengths) Format: [min1, max1, min2, max2, ...] pairs in microns

Returns: Vector of refined peak wavelengths in microns, or NULL on error

Note: The returned vector must be deallocated with cpl_vector_delete(); Peaks too close together (< 2 * spectral resolution) are rejected; Outliers are identified using 3-sigma clipping on wavelength shift and line width; Gaussian fitting uses a window of ±5 pixels around each initial peak position; Failed Gaussian fits result in peak rejection

Definition at line 729 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, BRK_WITH_ERROR, CATCH, CHECK_ERROR_STATE, eris_ifu_free_int_array(), eris_ifu_free_vector(), eris_ifu_lcorr_get_peak_positions(), fit_peak(), and TRY.

Referenced by eris_ifu_jitter_processSof().

◆ eris_ifu_lcorr_get_peak_positions()

cpl_array * eris_ifu_lcorr_get_peak_positions	(	const cpl_bivector *	spectrum,
		double	min_frac,
		cpl_vector *	range
	)

Detect emission line peak positions in a spectrum.

Identifies local maxima (peaks) in the input spectrum that exceed a minimum flux threshold. Peaks can be restricted to specified wavelength ranges. The algorithm finds peaks by detecting sign changes in the first derivative (positive to negative transition).

Parameters

spectrum	Input spectrum as bivector (X=wavelength, Y=flux)
min_frac	Minimum flux threshold as fraction of maximum flux (0.0-1.0)
range	Optional wavelength ranges to search (NULL for all wavelengths) Format: [min1, max1, min2, max2, ...] pairs in microns

Returns: Array of peak indices (positions in the spectrum vector), or NULL on error

Note: The returned array must be deallocated with cpl_array_delete(); Only flux values above (max_flux * min_frac) are considered; A peak is identified where derivative changes from positive to negative; If range is specified, peaks outside all ranges are ignored; The range vector must have an even number of elements

Definition at line 602 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_ERROR, BRK_IF_NULL, CATCH, CATCH_MSG, and TRY.

Referenced by eris_ifu_lcorr_get_peak_lambdas().

◆ eris_ifu_lcorr_open_debug_file()

void eris_ifu_lcorr_open_debug_file ( const char * filename )

open ASCII file to hold debug results

Parameters

filename input filename

Definition at line 1423 of file eris_ifu_lambda_corr.c.

◆ eris_ifu_lcorr_read_OH_reference_spectrum()

cpl_bivector * eris_ifu_lcorr_read_OH_reference_spectrum	(	const char *	filename,
		cpl_size	ext_number
	)

Read OH reference spectrum from FITS file.

Loads a reference OH sky emission spectrum from a FITS file and constructs a bivector with wavelength and flux values. The wavelength scale is derived from WCS keywords in the file's header.

Parameters

filename	Path to FITS file containing the reference spectrum
ext_number	FITS extension number to read (0 for primary HDU)

Returns: Bivector with X=wavelengths (microns) and Y=flux, or NULL on error

Note: The returned bivector must be deallocated with cpl_bivector_delete(); The file must contain FITS keywords: NAXIS1, CRVAL1, CDELT1, CRPIX1; CRPIX1 can be integer, float, or double type; Wavelength for pixel i is: lambda[i] = CRVAL1 + (i + 1 - CRPIX1) * CDELT1

Definition at line 499 of file eris_ifu_lambda_corr.c.

References ASSURE, BRK_IF_NULL, BRK_WITH_ERROR_MSG, CATCH, CATCH_MSG, CHECK_ERROR_STATE, and TRY.

Referenced by eris_ifu_jitter_processSof().

◆ fit_peak()

double fit_peak	(	const cpl_bivector *	spectrum,
		const cpl_size	size,
		double	lambda_in,
		int	half_width,
		double *	sigma_par
	)

fit a peak

Parameters

spectrum	input spectrum
size	size of input spectrum
lambda_in	input lambda near which peak is found
half_width	input half_with of range where fit is done
sigma_par	output sigma

Returns: position of peak maximum, 0 in case of failure.

Definition at line 1012 of file eris_ifu_lambda_corr.c.

References gauss1d_fnc(), and gauss1d_fncd().

Referenced by eris_ifu_lcorr_crosscorrelate_spectra(), and eris_ifu_lcorr_get_peak_lambdas().

◆ gauss1d_fnc()

int gauss1d_fnc	(	const double	x[],
		const double	a[],
		double *	result
	)

define a Gaussian profile

Parameters

x	File name of input FITS file holding the reference spectrum
a	minimum fraction
result	Gaussian profile

Returns: 1 in case of success, 0 otherwise.

Definition at line 940 of file eris_ifu_lambda_corr.c.

Referenced by fit_peak().

◆ gauss1d_fncd()

int gauss1d_fncd	(	const double	x[],
		const double	a[],
		double	result[]
	)

define a Gaussian profile

Parameters

x	File name of input FITS file holding the reference spectrum
a	minimum fraction
result	Gaussian profile

Returns: 1 in case of success, 0 otherwise.

Definition at line 969 of file eris_ifu_lambda_corr.c.

Referenced by fit_peak().

Functions

Detailed Description

Function Documentation

◆ eris_ifu_lcorr_close_debug_file()

◆ eris_ifu_lcorr_create_lambda_vector()

◆ eris_ifu_lcorr_create_object_mask()

◆ eris_ifu_lcorr_crosscorrelate_spectra()

◆ eris_ifu_lcorr_extract_spectrum()

◆ eris_ifu_lcorr_get()

◆ eris_ifu_lcorr_get_peak_lambdas()

◆ eris_ifu_lcorr_get_peak_positions()

◆ eris_ifu_lcorr_open_debug_file()

◆ eris_ifu_lcorr_read_OH_reference_spectrum()

◆ fit_peak()

◆ gauss1d_fnc()

◆ gauss1d_fncd()