IFU Jitter Processing Static Functions

Core jitter observation processing workflows and cube reconstruction. More...

Macros
#define	ERIS_IFU_SKIP_SKY_CORR_PLANES   75
	*static *‍/void

Functions
void	eris_ifu_jitter_free_sofStruct (struct sofStruct *sof_struct)
	Free and clean up SOF structure and all contained data.
void	eris_ifu_jitter_get_cube_type_string (cubeType type)
	Print cube type as string to log.
cubeType	eris_ifu_jitter_get_coadd_obj_type (cubeType type)
	Convert cube type to corresponding coadded cube type.
cubeType	eris_ifu_jitter_get_obj_type (sofModes mode)
	Get object cube type from SOF observation mode.
cubeType	eris_ifu_jitter_get_sky_type (sofModes mode)
	Get sky cube type from SOF observation mode.
cpl_error_code	eris_ifu_jitter_process_exposures (struct sofStruct *sof, struct stdParamStruct stdParams, struct paramStruct params, cpl_frameset *frameset, const cpl_parameterlist *parlist, const char *recipe_name, const char *context)
	Process all raw exposures into calibrated 3D data cubes.
cpl_error_code	eris_ifu_jitter_process_cubes (struct sofStruct *sof, struct stdParamStruct stdParams, struct paramStruct params, cpl_frameset *frameset, const cpl_parameterlist *parlist, const char *recipe_name, cubeType *obj_type)
	Process and combine data cubes with sky tweaking and DAR correction.
hdrl_image *	eris_ifu_jitter_subtract_background (skyTweakModes sky_tweak, int objIdx, struct sofStruct *sof, productDepthType productDepth)
	Subtract sky or dark background from raw exposure image.
hdrl_imagelist *	eris_ifu_jitter_build_cube (hdrl_image *inputImage, int sofIdx, struct sofStruct *sof, struct paramStruct params, bool doVelocityCorrection, cpl_polynomial *ohLambdaCorrection, productDepthType productDepth)
	Build 3D data cube from 2D detector image.
cpl_error_code	eris_image_get_valid_data_range (cpl_image *image, cpl_size *min, cpl_size *max)
	Determine valid data range in spectral direction (find NaN-dominated rows)
cpl_imagelist *	eris_ifu_jitter_reconstruct_cube (cpl_image *resampledDetImage, slitletDetectionModes mode, int fineTuneMode, double firstCol, cpl_vector *distancesV, cpl_bivector *positionsVV)
	Function to create a 3D-data cube from a re-sampled image.
cpl_error_code	eris_ifu_jitter_get_procatg_and_filename (cubeType type, char **proCatg, char **filenamePrefix)
	Get the value of the PRO.CATG and the filename as function of the type of cube.
cpl_error_code	eris_ifu_extract_spec (const cpl_imagelist *data_in, const cpl_imagelist *noise_in, cpl_image *mask, cpl_vector **spec_data_out, cpl_vector **spec_noise_out)
	Extract a spectrum from 3D data cube.
cpl_error_code	eris_ifu_extract_spec_fetch_params (const cpl_parameterlist *parlist, struct esParamStruct *params, const char *context)
	Fetch spectral extraction parameters from parameter list.
cpl_error_code	eris_ifu_jitter_extract (cpl_frameset *frameset, const cpl_parameterlist *parlist, cubeType obj_type, const char *pcatg, struct stdParamStruct stdParams, const char *pipefile_prefix, const char *context)
	Main spectral extraction function.
cpl_error_code	eris_ifu_jitter_extract_spec_processSof (cubeType obj_type, cpl_frameset *frames, struct esParamStruct params, struct esSofStruct *sof)
	Process SOF for spectral extraction.
cpl_error_code	eris_ifu_dar_correction (hdrl_imagelist *cube, cpl_propertylist *hdr, int method, double radius, int length)
	Apply Differential Atmospheric Refraction (DAR) correction.
cpl_error_code	eris_ifu_dar_cpl_shift (cpl_image *inImg, cpl_image *out1Img, cpl_image *out2Img, double xShift, double yShift, cpl_kernel kernelType, double width, cpl_size kernelSize)
	Apply DAR correction using CPL image shifting.
cpl_error_code	eris_ifu_dar_gsl_shift (cpl_image *inImg, cpl_image *outImg, double xShift, double yShift, const gsl_interp2d_type *T)
	Apply DAR correction using GSL 2D interpolation.
int	eris_frameset_count_tag (cpl_frameset *sof, const char *tag)
	Count frames with specified tag in frameset.
cpl_error_code	eris_frameset_duplicate_cube_tag (cpl_frameset *frameset, const char *pcatg, cpl_boolean apply_flat)
	Duplicate a cube file with different PRODCATG for coadded version.
cpl_error_code	eris_ifu_update_wcs_with_OCS_keywords (struct sofStruct *sof)
	Update WCS coordinates from OCS cumulative offset keywords.

Detailed Description

Core jitter observation processing workflows and cube reconstruction.

This module implements the complete data reduction workflow for jittered IFU observations, including data cube construction, sky subtraction, spectral extraction, and mosaicking.

Key Functionality:

• Exposure processing: dark/flat correction, distortion correction, wavelength resampling
• Cube reconstruction: conversion from brick-wall detector format to 3D data cubes
• Sky subtraction: multiple algorithms including Davies' method, Austrian skycorr, and automatic jitter
• OH line wavelength correction: spectral alignment using atmospheric OH emission lines
• DAR correction: compensation for differential atmospheric refraction
• Spectral extraction: point source and extended source extraction with various methods
• Cube combination: co-adding and mosaicking of multiple exposures
• WCS management: coordinate system updates from OCS keywords

Processing Workflow:

1. Load and validate SOF structure (eris_ifu_jitter_processSof from eris_ifu_jitter_interface.c)
2. Process individual exposures (eris_ifu_jitter_process_exposures)
   • Subtract sky/dark background
   • Apply flat field correction
   • Correct for bad pixels
   • Apply distortion correction
   • Resample wavelength scale
   • Reconstruct 3D cube
   • Apply OH-based wavelength correction
3. Process and combine cubes (eris_ifu_jitter_process_cubes)
   • Apply sky tweaking (Davies or Austrian method)
   • Handle automatic jitter sky subtraction
   • Apply DAR correction if requested
4. Extract spectra if point source mode
5. Co-add multiple exposures into final products

Sky Subtraction Methods:

• Standard: Paired object-sky observations
• Davies (sky_tweak=1): Spectral scaling and stretching of sky
• Austrian (sky_tweak=2): Pixel-by-pixel skycorr algorithm
• Automatic Jitter (aj-method 1-8): Sky estimation from object frames
  • Method 1: Use next object frame as sky
  • Method 2-3: Use median/mean of all sky frames
  • Method 4: User-specified rectangular box
  • Method 5-6: 4 or 8 regions at FOV edges
  • Method 7-8: Mask-based sky estimation (kappa-sigma or percentile clipping)

Data Structures:

• sofStruct: Main structure holding all calibration data and exposures
• exposureEntry: Individual exposure with associated cube and metadata
• paramStruct: Processing parameters
• cubeType: Enumeration of cube product types

Function Documentation

eris_frameset_count_tag()

int eris_frameset_count_tag	(	cpl_frameset *	sof,
		const char *	tag
	)

Count frames with specified tag in frameset.

Parameters

sof	Input frameset
tag	Tag to search for

Returns

Number of frames with matching tag, or -1 on error

Note

Simple utility function for frame counting

Definition at line 3661 of file eris_ifu_jitter_static.c.

Referenced by eris_stdstar_reduction_common().

eris_frameset_duplicate_cube_tag()

cpl_error_code eris_frameset_duplicate_cube_tag	(	cpl_frameset *	frameset,
		const char *	pcatg,
		cpl_boolean	apply_flat
	)

Duplicate a cube file with different PRODCATG for coadded version.

Parameters

frameset	input frameset containing data cube
pcatg	cube PRO.CATG
apply_flat	was the cube corrected by flat?

Returns

CPL_ERROR_NONE on success

Note

This function:

1. Finds frame with specified PRODCATG
2. Creates new filename with "_coadd" suffix
3. Copies file using system("cp ...") command
4. Updates PRODCATG in copied file
5. Adds new frame to frameset

Handles NOFLAT variants separately based on apply_flat parameter

Copies all extensions: primary HDU + 3 data extensions (DATA, ERROR, QUALITY)

Uses system() call (TODO: should use CPL file operations)

Definition at line 3700 of file eris_ifu_jitter_static.c.

Referenced by eris_stdstar_reduction_common().

eris_ifu_dar_correction()

cpl_error_code eris_ifu_dar_correction	(	hdrl_imagelist *	cube,
		cpl_propertylist *	hdr,
		int	method,
		double	radius,
		int	length
	)

Apply Differential Atmospheric Refraction (DAR) correction.

Parameters

cube	data cube to correct (modified in place)
hdr	FITS header with WCS info
shiftMethod	interpolation method for shifting [0-8]
shiftWidth	kernel radius for interpolation [pixels]
shiftLength	kernel length for interpolation

Returns

CPL_ERROR_NONE on success

Note

DAR causes wavelength-dependent image shifts due to atmospheric refraction

Correction algorithm:

1. Collapse cube to create reference wavelength image
2. For each wavelength plane:
   • Compute cross-correlation with reference to determine shift
   • Apply sub-pixel shift to align plane with reference

Shift methods: 0-8 correspond to different interpolation kernels

Uses either CPL shifting (shiftMethod < 5) or GSL interpolation (>= 5)

Reference wavelength typically chosen at center of band

Definition at line 3355 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, CATCH, CHECK_ERROR_STATE, eris_ifu_dar_cpl_shift(), eris_ifu_dar_gsl_shift(), eris_ifu_free_image(), eris_ifu_free_vector(), eris_ifu_lcorr_create_lambda_vector(), hdrl_dar_compute(), hdrl_dar_parameter_create(), hdrl_image_create(), hdrl_image_get_error(), hdrl_image_get_image(), hdrl_imagelist_get(), hdrl_imagelist_set(), hdrl_parameter_delete(), and TRY.

Referenced by eris_ifu_jitter_process_cubes().

eris_ifu_dar_cpl_shift()

cpl_error_code eris_ifu_dar_cpl_shift	(	cpl_image *	inImg,
		cpl_image *	out1Img,
		cpl_image *	out2Img,
		double	xShift,
		double	yShift,
		cpl_kernel	kernelType,
		double	width,
		cpl_size	kernelSize
	)

Apply DAR correction using CPL image shifting.

Parameters

cube	Data cube to correct (modified in place)
refImg	Reference image for cross-correlation
shiftMethod	CPL shift method [0-4]
shiftWidth	Kernel radius [pixels]
shiftLength	Kernel length

Returns

CPL_ERROR_NONE on success

Note

Uses cpl_image_correlate_create() to compute shifts

Uses cpl_image_shift() to apply sub-pixel shifts

Shift methods correspond to CPL_SHIFT_METHOD enum values

Definition at line 3504 of file eris_ifu_jitter_static.c.

References CATCH, CHECK_ERROR_STATE, eris_ifu_free_image(), eris_ifu_free_vector(), and TRY.

Referenced by eris_ifu_dar_correction().

eris_ifu_dar_gsl_shift()

cpl_error_code eris_ifu_dar_gsl_shift	(	cpl_image *	inImg,
		cpl_image *	outImg,
		double	xShift,
		double	yShift,
		const gsl_interp2d_type *	T
	)

Apply DAR correction using GSL 2D interpolation.

Parameters

cube	Data cube to correct (modified in place)
refImg	Reference image for cross-correlation
shiftMethod	Interpolation method (5=bilinear, 6=bicubic)
shiftWidth	Not used for GSL methods
shiftLength	Not used for GSL methods

Returns

CPL_ERROR_NONE on success

Note

Uses gsl_interp2d for sub-pixel interpolation

Method 5: Bilinear interpolation

Method 6: Bicubic interpolation

Generally provides smoother results than CPL methods

Definition at line 3586 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_dar_correction().

eris_ifu_extract_spec()

cpl_error_code eris_ifu_extract_spec	(	const cpl_imagelist *	data_in,
		const cpl_imagelist *	noise_in,
		cpl_image *	mask,
		cpl_vector **	spec_data_out,
		cpl_vector **	spec_noise_out
	)

Extract a spectrum from 3D data cube.

Parameters

	data_in	input 3D data cube
	noise_in	input 3D errors cube (can be NULL)
	mask	input pixel mask for weighted extraction (can be NULL)
[out]	spec_data_out	extracted spectrum (allocated by function)
[out]	spec_noise_out	error spectrum (allocated if noise_in provided)

Returns

cpl_error_code error status

Note

Extraction method:

• If mask provided: weighted sum, sum(data * mask) / sum(mask)
• If no mask: simple sum/average over spatial pixels

Skips bad pixels (marked in input image BPM) and non-finite values

Error propagation: sqrt(sum(err^2 * mask^2) / sum(mask^2))

Output vectors are allocated by this function and must be freed by caller

Loop over all wavelength planes (nz)

Definition at line 2654 of file eris_ifu_jitter_static.c.

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

Referenced by eris_ifu_lcorr_extract_spectrum().

eris_ifu_extract_spec_fetch_params()

cpl_error_code eris_ifu_extract_spec_fetch_params	(	const cpl_parameterlist *	parlist,
		struct esParamStruct *	params,
		const char *	context
	)

Fetch spectral extraction parameters from parameter list.

Parameters

parlist	input parameter list
params	output parameter structure (modified in place)
recipe_name	recipe name for parameter context

Returns

CPL_ERROR_NONE on success

Note

Extracts parameters:

• mask_method: "mask", "position", "max", "fit", "optimal"
• center: Center position as string "x,y" (parsed to integers)
• radius: Extraction radius [pixels]

Parses center string using sscanf to extract x,y coordinates

Validates that center coordinates are in valid range

Definition at line 3003 of file eris_ifu_jitter_static.c.

References BRK_WITH_ERROR_MSG, CATCH, CHECK_ERROR_STATE, and TRY.

Referenced by eris_ifu_jitter_extract().

eris_ifu_jitter_build_cube()

hdrl_imagelist * eris_ifu_jitter_build_cube	(	hdrl_image *	inputImage,
		int	sofIdx,
		struct sofStruct *	sof,
		struct paramStruct	params,
		bool	doVelocityCorrection,
		cpl_polynomial *	ohLambdaCorrection,
		productDepthType	productDepth
	)

Build 3D data cube from 2D detector image.

Parameters

inputImage	input image (brick-wall pattern, before re-sampling)
sofIdx	index of image in input sofStruct structure
sofStruct	data structure containing all input data
params	structure with all parameters required to reduce sci data
doVelocityCorrection	boolean switch to apply or not velocity corr
ohLambdaCorrection	polynomial coefficients with OH wave-cal corr
productDepth	product depth parameter

Returns

3D data cube as HDRL imagelist, or NULL on error

Note

This is the CORE cube building function that:

1. Divides by master flat field if available
2. Corrects bad pixels (multiple iterations if bpc_iter > 1)
3. Applies derotator correction (shifts distortion polynomials)
4. Warps image using distortion polynomials to correct geometric distortion
5. Applies velocity offset correction to wavelength scale if requested
6. Applies OH-based wavelength correction if polynomial provided
7. Resamples wavelength scale to regular grid
8. Reconstructs 3D cube from resampled brick-wall image
9. Creates corresponding bad pixel mask cube

Derotator correction compensates for spectrum wrapping across detector edges

Wavelength resampling uses eris_ifu_wave_resampled_arc_image()

Cube reconstruction uses eris_ifu_jitter_reconstruct_cube()

Updates sofIdx entry with:

• cubeHdr: Updated FITS header with WCS info
• cubeBpm: Bad pixel mask cube (replaces previous if exists)

Saves multiple debug products if productDepth >= PD_DEBUG

Definition at line 1880 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, CATCH, CHECK_ERROR_STATE, eris_check_error_code(), eris_ifu_bpm_correction(), eris_ifu_dist_warp_bpm(), eris_ifu_dist_warp_image(), eris_ifu_free_hdrl_image(), eris_ifu_free_image(), eris_ifu_free_propertylist(), eris_ifu_free_string(), eris_ifu_jitter_reconstruct_cube(), eris_ifu_mask_nans_in_cube(), eris_ifu_save_hdrl_image_dbg(), eris_ifu_warp_polynomial_image(), eris_ifu_wave_resampled_arc_image(), hdrl_image_create(), hdrl_image_div_image(), hdrl_image_duplicate(), hdrl_image_get_error(), hdrl_image_get_image(), hdrl_image_insert(), hdrl_image_new(), hdrl_imagelist_create(), hdrl_imagelist_get_size(), and TRY.

Referenced by eris_ifu_jitter_process_exposures().

eris_ifu_jitter_extract()

cpl_error_code eris_ifu_jitter_extract	(	cpl_frameset *	frameset,
		const cpl_parameterlist *	parlist,
		cubeType	obj_type,
		const char *	pcatg,
		struct stdParamStruct	stdParams,
		const char *	pipefile_prefix,
		const char *	context
	)

Main spectral extraction function.

Parameters

frameset	input frameset
obj_cube	object data cube
obj_cube_hdr	cube FITS header
params	extraction parameters
es_sof	extraction SOF structure
productDepth	product depth parameter

Returns

CPL_ERROR_NONE on success

Note

Creates extraction mask based on mask_method:

• "max": Find brightest pixel in collapsed cube
• "position": Use user-specified center
• "fit": Fit 2D Gaussian to find center
• "mask": Use provided mask image
• "optimal": Optimal extraction (not fully implemented)

Collapses cube to 2D image for mask creation

Creates circular mask with specified radius around center

Extracts spectrum using eris_ifu_extract_spec()

Populates es_sof with spectrum, error, totalFlux, wavelength

Definition at line 3101 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, CATCH, CATCH_MSG, eris_check_error_code(), eris_compute_psf_qc(), eris_ifu_extract_spec_fetch_params(), eris_ifu_free_bivector(), eris_ifu_free_hdrl_image(), eris_ifu_free_image(), eris_ifu_free_propertylist(), eris_ifu_free_vector(), eris_ifu_jitter_extract_spec_processSof(), eris_ifu_jitter_get_coadd_obj_type(), eris_ifu_jitter_get_cube_type_string(), eris_ifu_jitter_get_procatg_and_filename(), eris_ifu_save_deq_image(), hdrl_image_get_error(), hdrl_image_get_image(), hdrl_image_get_mask(), and TRY.

Referenced by eris_stdstar_reduction_common().

eris_ifu_jitter_extract_spec_processSof()

cpl_error_code eris_ifu_jitter_extract_spec_processSof	(	cubeType	obj_type,
		cpl_frameset *	frames,
		struct esParamStruct	params,
		struct esSofStruct *	sof
	)

Process SOF for spectral extraction.

Parameters

frameset	input frameset
obj_type	cube type
sof	input SOF structure
params	extraction parameters
recipe_name	recipe name
productDepth	product depth parameter

Returns

CPL_ERROR_NONE on success

Note

Sets up extraction SOF (es_sof) structure from main SOF

Handles both regular cubes and coadded cubes

Extracts framesets for OBJ, STD, and PSF observations

Calls eris_ifu_jitter_extract() to perform actual extraction

Calls eris_ifu_jitter_spec_save_products() to save results

Definition at line 3263 of file eris_ifu_jitter_static.c.

References BRK_IF_NULL, BRK_WITH_ERROR_MSG, CATCH, CHECK_ERROR_STATE, eris_check_error_code(), eris_ifu_jitter_get_procatg_and_filename(), eris_ifu_load_deq_hdrl_imagelist(), hdrl_imagelist_get_size(), hdrl_imagelist_get_size_x(), hdrl_imagelist_get_size_y(), and TRY.

Referenced by eris_ifu_jitter_extract().

eris_ifu_jitter_free_sofStruct()

void eris_ifu_jitter_free_sofStruct

(

struct sofStruct *

sof_struct

)

Free and clean up SOF structure and all contained data.

Parameters

sof_struct

SOF structure to free (can be NULL)

Note

This function deallocates all memory associated with the SOF structure including:

• Exposure table with all raw images, cubes, headers, and masks
• Master calibration frames (dark, flat)
• Wavelength map and distortion polynomials
• Bad pixel masks and DQI images
• OH reference data

Some members (frame, rawImage) are commented out to avoid segmentation faults, suggesting potential ownership issues

After freeing, the structure pointer is set to NULL (but this only affects local copy)

Definition at line 154 of file eris_ifu_jitter_static.c.

References hdrl_image_delete(), and hdrl_imagelist_delete().

Referenced by eris_stdstar_reduction_common().

eris_ifu_jitter_get_coadd_obj_type()

cubeType eris_ifu_jitter_get_coadd_obj_type

(

cubeType

type

)

Convert cube type to corresponding coadded cube type.

Parameters

type	Input cube type

Returns

Corresponding coadded cube type (e.g., OBJECT_CUBE -> OBJECT_CUBE_COADD)

Note

Returns OBJECT_CUBE_COADD as default for unrecognized types

Preserves NOFLAT variants (STD_FLUX_CUBE_NOFLAT -> STD_FLUX_CUBE_COADD_NOFLAT)

Definition at line 324 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_jitter_extract().

eris_ifu_jitter_get_cube_type_string()

void eris_ifu_jitter_get_cube_type_string

(

cubeType

type

)

Print cube type as string to log.

Parameters

type	Cube type enumeration value

Note

Outputs an informational message with the cube type name for debugging purposes

Handles all defined cube types including object, sky, standard, PSF, DAR, and coadded variants

Definition at line 230 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_jitter_extract(), and eris_stdstar_reduction_common().

eris_ifu_jitter_get_obj_type()

cubeType eris_ifu_jitter_get_obj_type

(

sofModes

mode

)

Get object cube type from SOF observation mode.

Parameters

mode	SOF observation mode (SCIENCE, STD, STD_FLUX, PSF, etc.)

Returns

Corresponding object cube type

Note

Maps observation modes to cube types:

• SCIENCE -> OBJECT_CUBE
• STD -> STD_CUBE
• STD_FLUX -> STD_FLUX_CUBE
• PSF -> PSF_CUBE
• default -> OBJECT_CUBE

Definition at line 396 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_jitter_process_cubes(), and eris_ifu_jitter_process_exposures().

eris_ifu_jitter_get_procatg_and_filename()

cpl_error_code eris_ifu_jitter_get_procatg_and_filename	(	cubeType	type,
		char **	proCatg,
		char **	filenamePrefix
	)

Get the value of the PRO.CATG and the filename as function of the type of cube.

Parameters

	type	the cube type
[out]	proCatg	cube PRO.CATG (caller must free)
[out]	filenamePrefix	cube filename prefix (caller must free)

Returns

CPL_ERROR_NONE on success

Note

Maps each cubeType enum to appropriate PRODCATG and filename

Handles all cube types: OBJECT, STD, PSF, SKY, DAR, TWEAKED, BPM, JITTER

Also handles COADD variants and NOFLAT variants

Strings returned via proCatg and filenamePrefix must be freed by caller

Definition at line 2514 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_combine(), eris_ifu_jitter_extract(), eris_ifu_jitter_extract_spec_processSof(), eris_ifu_jitter_process_cubes(), and eris_stdstar_reduction_common().

eris_ifu_jitter_get_sky_type()

cubeType eris_ifu_jitter_get_sky_type

(

sofModes

mode

)

Get sky cube type from SOF observation mode.

Parameters

mode	SOF observation mode (SCIENCE, STD, STD_FLUX, PSF, etc.)

Returns

Corresponding sky cube type

Note

Maps observation modes to sky cube types:

• SCIENCE -> SKY_OBJECT_CUBE
• STD -> SKY_STD_CUBE
• STD_FLUX -> SKY_STD_FLUX_CUBE
• PSF -> SKY_PSF_CUBE
• default -> SKY_OBJECT_CUBE

Definition at line 437 of file eris_ifu_jitter_static.c.

Referenced by eris_ifu_jitter_process_cubes(), and eris_ifu_jitter_process_exposures().

eris_ifu_jitter_process_cubes()

cpl_error_code eris_ifu_jitter_process_cubes	(	struct sofStruct *	sof,
		struct stdParamStruct	stdParams,
		struct paramStruct	params,
		cpl_frameset *	frameset,
		const cpl_parameterlist *	parlist,
		const char *	recipe_name,
		cubeType *	obj_type
	)

Process and combine data cubes with sky tweaking and DAR correction.

Parameters

sof	SOF structure containing all exposures and their cubes
stdParams	Standard pipeline parameters
params	Jitter-specific processing parameters
frameset	Input frameset for DFS compliance
parlist	Recipe parameter list
recipe_name	Recipe name for output products
obj_type	Output: determined object cube type (modified in place)

Returns

CPL_ERROR_NONE on success, otherwise an error code

Note

This is a MAIN processing function that:

1. Loops through all object exposures
2. Applies sky tweaking if requested:
   • Davies method: Spectral scaling and stretching
   • Austrian method: Pixel-by-pixel skycorr algorithm
3. Handles automatic jitter sky subtraction (aj-method parameter)
4. Applies DAR correction if enabled
5. Saves intermediate products (tweaked cubes, DAR-corrected cubes)
6. Ensures at least one cube product exists for extraction

Sky tweaking requires paired object-sky observations

Automatic jitter (aj-method > 3) works without sky frames

DAR correction uses parameters: darShiftMethod, darShiftWidth, darShiftLength

Uses TRY/CATCH error handling with detailed error messages

Definition at line 1347 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, BRK_WITH_ERROR_MSG, CATCH, CATCH_MSGS, CHECK_ERROR_STATE, eris_ifu_dar_correction(), eris_ifu_extract_frameset(), eris_ifu_free_imagelist(), eris_ifu_free_mask(), eris_ifu_free_parameterlist(), eris_ifu_free_string(), eris_ifu_free_table(), eris_ifu_jitter_get_obj_type(), eris_ifu_jitter_get_procatg_and_filename(), eris_ifu_jitter_get_sky_type(), eris_ifu_sky_tweak(), eris_ifu_split_hdrl_imagelist(), hdrl_image_reject_from_mask(), hdrl_imagelist_create(), hdrl_imagelist_get(), hdrl_imagelist_get_size(), hdrl_imagelist_get_size_x(), hdrl_imagelist_get_size_y(), sc_skycorr(), and TRY.

Referenced by eris_stdstar_reduction_common().

eris_ifu_jitter_process_exposures()

cpl_error_code eris_ifu_jitter_process_exposures	(	struct sofStruct *	sof,
		struct stdParamStruct	stdParams,
		struct paramStruct	params,
		cpl_frameset *	frameset,
		const cpl_parameterlist *	parlist,
		const char *	recipe_name,
		const char *	context
	)

Process all raw exposures into calibrated 3D data cubes.

Parameters

sof	SOF structure containing all exposures and calibrations
stdParams	Standard pipeline parameters
params	Jitter-specific processing parameters
frameset	Input frameset for DFS compliance
parlist	Recipe parameter list
recipe_name	Recipe name for output products
context	Parameter context string (e.g., "eris.eris_ifu_jitter")

Returns

CPL_ERROR_NONE on success, otherwise an error code

Note

This is a MAIN processing function that:

1. Loops through all object and sky exposures in the SOF
2. For each exposure:
   • Subtracts sky/dark background if available
   • Builds initial 3D cube via eris_ifu_jitter_build_cube()
   • Computes OH-based wavelength correction if OH reference available
   • Rebuilds cube with OH correction applied
   • Saves auxiliary cube products if productDepth >= PD_AUXILLIARY
   • Optionally removes NaN-heavy spectral planes (chop-nan parameter)
3. Updates WCS from OCS keywords if USE_OCS environment variable set

OH alignment can be controlled by parameters:

• skip_oh_align: Skip all OH alignment
• skip_sky_oh_align: Skip OH alignment for sky frames only
• oh_align_poly_order: Polynomial order for OH fitting [0-3]

Output cubes are stored in sof->exposureTable[ix].cube for later processing

Uses TRY/CATCH error handling for robustness

Definition at line 704 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, CATCH, eris_check_error_code(), eris_ifu_append_qc_float(), eris_ifu_cube_trim_nans(), eris_ifu_free_hdrl_image(), eris_ifu_free_hdrl_imagelist(), eris_ifu_free_polynomial(), eris_ifu_get_band(), eris_ifu_get_plane_cut_min_max(), eris_ifu_jitter_build_cube(), eris_ifu_jitter_get_obj_type(), eris_ifu_jitter_get_sky_type(), eris_ifu_jitter_subtract_background(), eris_ifu_lcorr_get(), eris_ifu_update_wcs_with_OCS_keywords(), hdrl_imagelist_get_size(), and TRY.

Referenced by eris_stdstar_reduction_common().

eris_ifu_jitter_reconstruct_cube()

cpl_imagelist * eris_ifu_jitter_reconstruct_cube	(	cpl_image *	resampledDetImage,
		slitletDetectionModes	mode,
		int	fineTuneMode,
		double	firstCol,
		cpl_vector *	distancesV,
		cpl_bivector *	positionsVV
	)

Function to create a 3D-data cube from a re-sampled image.

Parameters

resampledDetImage	the re-sampled image
mode	parameter to control the slitlet detection algorithm used
fineTuneMode	Specifies the row interpolation mode using GSL routines 0: no interpolation >2: polynomial interpolation, polynomial degree is interType-1 2: linear interpolation -1: Cubic spline with natural boundary conditions -2: cubic spline with periodic boundary conditions -3: Non-rounded Akima spline with natural boundary conditions. -4: Non-rounded Akima spline with periodic boundary conditions. -5: Steffen's method guarantees the monotonicity of the interpolating function between the given data points
firstCol	first column of each slitlet used to re-sample image
distancesV	output computed slitlets distances (for DISTANCES mode, can be NULL)
positionsVV	output computed slutlets positions (for EDGES mode, can be NULL)

Returns

reconstructed 3D data cube (cpl_imagelist object)

Note

This function converts the "brick-wall" detector format to a proper 3D cube

Three modes supported:

• DISTANCES: Use measured slitlet separations from calibration
• EDGES: Use measured slitlet edge positions from calibration
• GRID: Simple grid-based (new ERIS method, distancesV must be NULL)

Output cube dimensions: [onx, ony, onz] where:

• onx = input_x / SLITLET_CNT
• ony = SLITLET_CNT * 2 (factor of 2 to make square spaxels)
• onz = input_y (spectral direction)

Flux is divided by 2 when expanding Y dimension to conserve flux

Applies fine-tuning interpolation if fineTuneMode != 0

For GRID mode (new ERIS), x-axis is flipped to correct east direction

Definition at line 2296 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, BRK_WITH_ERROR_MSG, CATCH, eris_ifu_1d_interpolation(), eris_ifu_free_imagelist(), eris_ifu_mask_nans_in_cube(), and TRY.

Referenced by eris_ifu_jitter_build_cube().

eris_ifu_jitter_subtract_background()

hdrl_image * eris_ifu_jitter_subtract_background	(	skyTweakModes	sky_tweak,
		int	objIdx,
		struct sofStruct *	sof,
		productDepthType	productDepth
	)

Subtract sky or dark background from raw exposure image.

Parameters

sky_tweak	Sky tweaking mode (NONE, DAVIES, AUSTRIAN)
objIdx	Index of object exposure in SOF
sof	SOF structure containing calibrations and exposures
productDepth	Product depth parameter for debug output

Returns

Background-subtracted HDRL image, or NULL on error

Note

Background subtraction strategy:

1. If sky_tweak == NONE:
   • Use paired sky frame if available (objEntry->skyIndex >= 0)
   • Otherwise use master dark if available
2. If sky_tweak != NONE, return raw image without subtraction (sky subtraction will be done later via tweaking)

Creates DQI (Data Quality Image) updates for new bad pixels

Saves debug products if productDepth >= PD_DEBUG

The returned image must be deleted by the caller

Memory for the image is allocated by this function

Definition at line 1773 of file eris_ifu_jitter_static.c.

References BRK_IF_ERROR, BRK_IF_NULL, CATCH, eris_ifu_free_image(), eris_ifu_free_mask(), eris_ifu_free_string(), eris_ifu_save_hdrl_image_dbg(), hdrl_image_delete(), hdrl_image_duplicate(), hdrl_image_get_mask(), hdrl_image_sub_image(), and TRY.

Referenced by eris_ifu_jitter_process_exposures().

eris_ifu_update_wcs_with_OCS_keywords()

cpl_error_code eris_ifu_update_wcs_with_OCS_keywords

(

struct sofStruct *

sof

)

Update WCS coordinates from OCS cumulative offset keywords.

Parameters

sof	SOF structure with exposure table

Returns

CPL_ERROR_NONE on success

Note

This function corrects WCS coordinates using telescope offset information:

1. Finds reference exposure (first with CUMOFFS1=CUMOFFS2=0, or first exposure)
2. Computes reference position: CRVAL_ref = CRVAL - CUMOFFS/3600
3. Updates all exposures: CRVAL_new = CRVAL_ref + CUMOFFS/3600

Only active if USE_OCS environment variable is set

CUMOFFS1/CUMOFFS2 are cumulative telescope offsets in arcsec

Corrects both CRVAL1 (RA) and CRVAL2 (DEC) keywords

Logs detailed before/after coordinates for verification

Definition at line 3815 of file eris_ifu_jitter_static.c.

References CATCH, CHECK_ERROR_STATE, and TRY.

Referenced by eris_ifu_jitter_process_exposures().

eris_image_get_valid_data_range()

cpl_error_code eris_image_get_valid_data_range	(	cpl_image *	image,
		cpl_size *	min,
		cpl_size *	max
	)

Determine valid data range in spectral direction (find NaN-dominated rows)

Parameters

image	Input 2D image to analyze
min	Output: minimum valid row index (modified in place)
max	Output: maximum valid row index (modified in place)

Returns

CPL_ERROR_NONE on success

Note

Scans first and last 200 rows to find rows with >50% NaN pixels

Sets min to last NaN-dominated row at start

Sets max to first NaN-dominated row at end

Used to trim edge planes in wavelength direction where calibration is poor

Definition at line 2222 of file eris_ifu_jitter_static.c.