Functions
cpl_error_code	moo_apply_flat (moo_ext ext, moo_ext flat, moo_f2f *f2f)
	Divide spectra by 1D flat-field.

cpl_error_code	moo_apply_p2p (moo_det flat, moo_det p2pmap)
	Divide DET by the pixel-to-pixel variation map.

cpl_error_code	moo_calib_flux (moo_rbn rbn, moo_atm atm, moo_resp *resp)
	Apply the relative flux calibration to 1D rebinned spectra.

moo_sci *	moo_coadd (moo_scilist scilist, moo_coadd_params params, const char *filename)
	Co-add reduced science frames in SCI format.

moo_sci *	moo_combine_pair (moo_rbn nod_rbn, moo_rbn sky_rbn, moo_rbn obj_rbn, moo_target_table target_table, moo_f2f f2f, const cpl_frame solflux_frame, const cpl_frame airglow_group_frame, const cpl_frame airglow_var_frame, moo_combine_pair_params combine_pair_params, moo_sub_sky_stare_params sky_params, const char filename, moo_products products, const cpl_frame *ref_frame)
	Combine the extracted spectra from a same objec.

moo_rbn *	moo_combine_sky (moo_rbnlist *rbnlist)
	Combine RBN sky frames.

moo_f2f *	moo_compute_fibtrans (moo_ext ext, moo_compute_fibtrans_params params, const char *filename)
	Computes fibre-to-fibre relative transmission table.

cpl_error_code	moo_reproject_model (moo_det flat1, moo_loc loc1, moo_psf model_flat1, const char filename)
	Reporject a model on detector.

moo_det *	moo_compute_p2p (moo_det flat1, moo_loc loc1, moo_psf model_flat1, moo_det flat2, moo_loc loc2, moo_psf model_flat2)
	To compute pixel-to-pixel variation map.

moo_resp *	moo_compute_resp (moo_scilist scilist, moo_atm atm, moo_flx flx, moo_compute_resp_params params)
	Compute instrumental response.

float *	moo_compute_slitoffset (moo_det det, moo_loc loc, moo_compute_slitoffset_params *params)
	Compute slit offset in LOC.

cpl_error_code	moo_correct_tell (moo_rbn rbn, moo_telluric tell)
	Apply the telluric correction to 1D rebinned spectra.

cpl_error_code	moo_correct_tell_science (moo_sci sci, moo_telluric tell)
	Apply the telluric correction to SCI.

cpl_error_code	moo_create_s1d (cpl_frame sci_frame, moo_create_s1d_params params, const char tag, moo_products products)
	Apply the telluric correction to SCI.

cpl_error_code	moo_correct_bias (moo_det det, const cpl_frame masterbias_frame, moo_correct_bias_params *params)
	Subtracts the Master Bias frame from a DET frame.

cpl_error_code	moo_correct_dark (moo_det det, moo_det detoff, const cpl_frame masterDarkVis, const cpl_frame masterDarkNir)
	Subtracts the master dark frame from a frame after scaling for exposure time (RI). Subtract OFF frame from ON frame (YJ, H)

cpl_error_code	moo_correct_detlin (moo_det det, const cpl_frame cube_frame)
	Apply the detector linearity correction.

cpl_error_code	moo_single_compute_noise_map (moo_single single, moo_nos_params params, cpl_imagelist list, cpl_imagelist qlist)
	Calculates the noisey bad pixel mask for one extension.

cpl_error_code	moo_compute_noise_map (moo_det det, moo_detlist darkList, moo_masklist cosmiclist, moo_nos_params params)
	Calculates the noisey bad pixel mask.

cpl_error_code	moo_compute_hot_map (moo_det det, moo_hot_params params)
	Calculates the hot bad pixel mask.

moo_ext *	moo_extract (moo_det det, moo_loc loc, moo_psf master_flat, moo_extract_params params, const char *filename)
	extract the 1D spectrum of fibres

cpl_error_code	moo_flat_shift_compute (moo_det det, moo_loc ff_trace)
	Compute the shift between FF_TRACE and FLAT.

moo_loc *	moo_localise (moo_det det, const cpl_frame guess_loc, moo_localise_params params, const char locname)
	To localise the centroid of fibre spectrum on frames.

moo_psf *	moo_model_flat (moo_det det, moo_loc loc, moo_model_flat_params params, const char filename)
	To extract 2D FF and model it, resulting MASTER_FLAT.

moo_molectable *	moo_molecfit_model (const cpl_frame sci_frame, const char modename, const cpl_frame molecule_frame, const cpl_frame winc_frame, moo_molectable pmt_atm_fitted, moo_molectable best_fitted_model, moo_molecfit_model_params *params)
	Apply the relative flux calibration to 1D rebinned spectra.

moo_telluric *	moo_molecfit_calctrans (const cpl_frame rbn_frame, const char modename, const cpl_frame molecules_frame, const cpl_frame atm_frame, const cpl_frame best_fit_frame, const cpl_frame kernel_lib_frame, moo_molecfit_calctrans_params *params)
	Apply the molcecfit calctrans to the RBN to compute telle telluric correction.

moo_det *	moo_prepare (const cpl_frame rawframe, const char const badpixmask_rp, const char const badpixmask_nl, const cpl_frame masterbias, const cpl_frame cube_frame, moo_prepare_params params)
	This function transforms RAW frames in DET frames attaching the default bad pixel map and an error image.

moo_det *	moo_prepare_adu (const cpl_frame rawframe, const char const badpixmask_rp, moo_prepare_params *params)
	This function transforms RAW frames in DET ADU frames attaching the default bad pixel.

moo_rbn *	moo_rebin (moo_ext ext, moo_map wmap, moo_spectral_format sformat, moo_rebin_params params, const char *filename)
	Rebin an EXT spectra in RBN format.

moo_det *	moo_remove_CRH (moo_detlist detlist, moo_masklist cosmiclist, moo_crh_params *params)
	Remove CRH in single frames or in a combination of multiple frames.

cpl_array *	moo_select_sky (const char targname, int indextarg, int obj_index, double obj_targalpha, double obj_targdelta, cpl_table target_table, const char index_colname, cpl_table sky_stare_table, moo_detector_type type, int maxdistslit, double mintrans, int min_sky, double radius, double step_r, int target_table_idx, moo_f2f f2f, cpl_array allsky_indexes)
	This function selects sky fibres around a target object.

moo_sci *	moo_sub_sky_stare (moo_rbn obja_rbn, moo_target_table target_table, moo_rbn objb_rbn, moo_f2f f2f, const cpl_frame solflux_frame, const cpl_frame airglow_group_frame, const cpl_frame airglow_var_frame, moo_sub_sky_stare_params params, const char *filename, int ispaired)
	This function subtracts the sky in wavelength calibrated and extracted science frames obtain in Stare mode observations.

moo_det *	moo_subtract_nod (moo_det object, moo_det sky, const char *filename)
	Sky from object subtraction.

moo_map *	moo_wavesol (moo_ext arc_ext, const char lineCatname, moo_spectral_format sformat, moo_loc loc, moo_map wmap, moo_wavesol_params params)
	Computes the wavelength solution from 1D extracted arc spectra.

Detailed Description

Function Documentation

◆ moo_apply_flat()

cpl_error_code moo_apply_flat	(	moo_ext *	ext,
		moo_ext *	flat,
		moo_f2f *	f2f
	)

Divide spectra by 1D flat-field.

Parameters

ext	EXT extracted to flatfield
flat	EXT extracted flatfield
f2f	fibre-to-fibre relative transmission table

Returns: cpl_error_code or CPL_ERROR_NONE

This function performs a simple division by a flat field.

Bad pixels flags:

BADPIX_CALIB_DEFECT where division failed.

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 182 of file moo_apply_flat.c.

References MOO_BADPIX_LOW_QE, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_detector_get_extname(), moo_ext_get_fibre_table(), moo_ext_load_single(), moo_f2f_get_trans(), moo_f2f_order_by_index(), moo_fibres_table_add_f2f_cols(), and moo_fibres_table_get_spectro_index().

◆ moo_apply_p2p()

cpl_error_code moo_apply_p2p	(	moo_det *	flat,
		moo_det *	p2pmap
	)

Divide DET by the pixel-to-pixel variation map.

Parameters

flat	DET which is divided
p2pmap	DET pixel to pixel variation map

Returns: cpl_error_code or CPL_ERROR_NONE

This function performs a simple division by a P2P map.

Bad pixels flags:

BADPIX_CALIB_DEFECT where division failed.

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 122 of file moo_apply_p2p.c.

References MOO_BADPIX_GOOD, moo_det_get_primary_header(), moo_det_load_single(), moo_detector_get_extname(), and moo_qc_set_is_p2pcor().

◆ moo_calib_flux()

cpl_error_code moo_calib_flux	(	moo_rbn *	rbn,
		moo_atm *	atm,
		moo_resp *	resp
	)

Apply the relative flux calibration to 1D rebinned spectra.

Parameters

rbn	RBN spectra
atm	Atmospheric extinction table
resp	Instrumental response

Returns: Flux calibrated frame

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 143 of file moo_calib_flux.c.

References MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_pfits_get_cd1_1(), moo_pfits_get_crpix1(), moo_pfits_get_crval1(), moo_pfits_get_dit(), moo_pfits_get_exptime(), moo_pfits_get_ndit(), moo_pfits_get_tel_airm_end(), moo_pfits_get_tel_airm_start(), moo_rbn_get_fibre_table(), moo_rbn_get_primary_header(), moo_rbn_load_single(), moo_rbn_single_get_header(), moo_rbn_single_get_image(), moo_resp_get_colname(), and moo_resp_get_table().

◆ moo_coadd()

moo_sci * moo_coadd	(	moo_scilist *	scilist,
		moo_coadd_params *	params,
		const char *	filename
	)

Co-add reduced science frames in SCI format.

Parameters

scilist	List of SCI files
params	coadd params
filename	name of result file

Returns: the SCI result

_Flags considered as bad : BADPIX_COSMETIC | BADPIX_HOT

Bad pixels flags:

BADPIX_COSMIC_UNREMOVED is set in SIGCLIP mode

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the SCI list have a size

Definition at line 134 of file moo_coadd.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_fits_create(), moo_imagelist_collapse_bitwiseor(), moo_pfits_update_ncoadd(), moo_sci_add_single(), moo_sci_add_target_table(), moo_sci_create(), moo_sci_delete(), moo_sci_get_single(), moo_sci_get_target_table(), moo_sci_new(), moo_sci_save(), moo_sci_single_get_header(), moo_sci_single_get_image(), moo_sci_single_get_qual(), moo_sci_single_get_sky(), moo_sci_single_new(), moo_scilist_get(), moo_scilist_get_single(), moo_scilist_get_size(), moo_scilist_load_single(), moo_target_table_find_index(), moo_target_table_find_target(), and moo_target_table_remove_coadd_cols().

◆ moo_combine_pair()

moo_sci * moo_combine_pair	(	moo_rbn *	nod_rbn,
		moo_rbn *	sky_rbn,
		moo_rbn *	obj_rbn,
		moo_target_table *	target_table,
		moo_f2f *	f2f,
		const cpl_frame *	solflux_frame,
		const cpl_frame *	airglow_group_frame,
		const cpl_frame *	airglow_var_frame,
		moo_combine_pair_params *	combine_pair_params,
		moo_sub_sky_stare_params *	sky_params,
		const char *	filename,
		moo_products *	products,
		const cpl_frame *	ref_frame
	)

Combine the extracted spectra from a same objec.

Parameters

nod_rbn	_RBN Wavelength calibrated science spectra from NOD
sky_rbn	_RBN Wavelength calibrated science spectra from SKY
obj_rbn	_RBN Wavelength calibrated science spectra from OBJECT
target_table	TARGET_TABLE Attached target table
f2f	F2F fibre to fibre table
solflux_frame	the monthly averages of solar radio flux at 10.7 cm frame
airglow_group_frame	the airglow line list frame (use in subsky)
airglow_var_frame	the airglow scaling parameters frame (use in subsky)
combine_pair_params	the combine pair parameters
sky_params	the sub sky stare parameters
filename	the SCI filename
products	the product structure to save file
ref_frame	the reference frame to produce product KW

Returns: the SCI result

_Flags considered as bad : MOO_BADPIX_OUTSIDE_DATA_RANGE, MOO_BADPIX_CALIB_DEFECT

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 802 of file moo_combine_pair.c.

References moo_products_add_sci(), moo_sci_delete(), moo_sci_save(), and moo_sub_sky_stare().

◆ moo_combine_sky()

moo_rbn * moo_combine_sky ( moo_rbnlist * rbnlist )

Combine RBN sky frames.

Parameters

rbnlist list of RBN frames

Returns: the RBN result

_Flags considered as bad : BADPIX_COSMETIC

Bad pixels flags:

BADPIX_COSMIC_UNREMOVED is set in SIGCLIP mode

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if RBN list size is lower or equal to zero

Definition at line 208 of file moo_combine_sky.c.

References MOO_BADPIX_GOOD, moo_qc_set_ncom(), moo_rbn_delete(), moo_rbn_get_fibre_table(), moo_rbn_new(), and moo_rbnlist_get().

◆ moo_compute_fibtrans()

moo_f2f * moo_compute_fibtrans	(	moo_ext *	ext,
		moo_compute_fibtrans_params *	params,
		const char *	filename
	)

Computes fibre-to-fibre relative transmission table.

Parameters

ext	EXT spectra from which computes transmission
params	fibre transmission parameters
filename	name of the result F2F

Returns: the result F2F

The function expects as input flat-field data obtained with a uniformly illuminated field of view. Then it decouples the relative intensity and the shape of the extracted flat-field spectra into a fibre-to-fibre relative transmission table and a normalised extracted Flat-field respectively.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if an input pointer is NULL

Definition at line 193 of file moo_compute_fibtrans.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_COSMETIC, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_detector_get_extname(), moo_ext_get_fibre_table(), moo_ext_load_single(), moo_f2f_create(), moo_f2f_delete(), and moo_f2f_set_trans().

◆ moo_compute_hot_map()

cpl_error_code moo_compute_hot_map	(	moo_det *	det,
		moo_hot_params *	params
	)

Calculates the hot bad pixel mask.

Parameters

det	DET Average dark frame
params	hot map parameters

Returns: the error code

This function searches for hot bad pixels in a master dark frame by applying an iterative kappa-sigma clipping algorithm. The QUAL extension of det frame is updated.

Bad pixels flags:

BADPIX_HOT

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 830 of file moo_drl.c.

References MOO_BADPIX_COSMETIC, MOO_BADPIX_COSMIC_UNREMOVED, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), and moo_detector_get_extname().

◆ moo_compute_noise_map()

cpl_error_code moo_compute_noise_map	(	moo_det *	det,
		moo_detlist *	darkList,
		moo_masklist *	cosmiclist,
		moo_nos_params *	params
	)

Calculates the noisey bad pixel mask.

Parameters

det	DET Average dark frame
darkList	series of individual DET dark frames
cosmiclist	series of individual MASK of dark frames
params	noise map parameters

Returns: the error code

This function searches for static bad pixels in stacks of dark frames taken with equal exposure times. The noise in each pixel stack is computed and compared to the mean noise and a pixel is declared bad if the deviation exceeds nos-clip-sigma. The QUAL extension of det frame is updated.

_Flags considered as bad : BADPIX_COSMETIC | BADPIX_COSMIC_UNREMOVED | BADPIX_HOT

Bad pixels flags:

BADPIX_NOISY

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the frame is darkList size < 3
CPL_ERROR_ILLEGAL_INPUT if the frame is not tagged has MASTER BIAS

Definition at line 629 of file moo_drl.c.

References MOO_BADPIX_COSMETIC, MOO_BADPIX_COSMIC_UNREMOVED, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), moo_detlist_free_single(), moo_detlist_get_single_data(), moo_detlist_get_single_qual(), moo_detlist_get_size(), moo_detlist_load_single(), moo_mask_get(), moo_mask_to_badpix(), moo_masklist_get(), and moo_single_compute_noise_map().

◆ moo_compute_p2p()

moo_det * moo_compute_p2p	(	moo_det *	flat1,
		moo_loc *	loc1,
		moo_psf *	model_flat1,
		moo_det *	flat2,
		moo_loc *	loc2,
		moo_psf *	model_flat2
	)

To compute pixel-to-pixel variation map.

Parameters

flat1	DET first flat field
loc1	LOC localisation of the first flat field
model_flat1	PSF model of the first flat field
flat2	DET second flat field
loc2	LOC localisation of the second flat field
model_flat2	PSF model of the second flat field

Returns: DET the pixel to pixel variation map

The function co-adds two preprocessed flat-field frames at two slit positions is order to increase the illumination coverage of the detectors, and it co-adds as well the corresponding modeled FFs. Then it derives the pixel-to-pixel variation map.

Bad pixels flags:

BADPIX_CALIB_DEFECT

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if first localisation has not a fibres table

Definition at line 398 of file moo_compute_p2p.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_LOW_QE, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_delete(), moo_det_load_single(), moo_det_new(), moo_detector_get_extname(), moo_fits_create(), moo_fits_write_extension_image(), moo_loc_get_fibre_table(), moo_loc_get_single(), and moo_psf_get_single().

◆ moo_compute_resp()

moo_resp * moo_compute_resp	(	moo_scilist *	scilist,
		moo_atm *	atm,
		moo_flx *	flx,
		moo_compute_resp_params *	params
	)

Compute instrumental response.

Parameters

scilist	List of sky subtracted spectra of the standard star
atm	Atmospheric extinction table
flx	Standard star flux table
params	Compute response parameters

Returns: the response

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the SCI list have a size

Definition at line 257 of file moo_compute_resp.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_COSMETIC, MOO_BADPIX_HOT, MOO_BADPIX_LOW_QE, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_median_filter(), moo_pfits_get_cd1_1(), moo_pfits_get_tel_airm_end(), moo_pfits_get_tel_airm_start(), moo_resp_create(), moo_resp_get_table(), moo_sci_get_single(), moo_sci_get_target_table(), moo_sci_single_get_header(), moo_scilist_get(), moo_scilist_get_size(), and moo_target_table_find_index().

◆ moo_compute_slitoffset()

float * moo_compute_slitoffset	(	moo_det *	det,
		moo_loc *	loc,
		moo_compute_slitoffset_params *	params
	)

Compute slit offset in LOC.

Parameters

det	the DET frame
loc	the LOC frame
params	the compute slit offset parameters

Returns: the slit offset by detector

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 197 of file moo_compute_slitoffset.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_COSMETIC, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), and moo_loc_get_single().

◆ moo_correct_bias()

cpl_error_code moo_correct_bias	(	moo_det *	det,
		const cpl_frame *	masterbias_frame,
		moo_correct_bias_params *	params
	)

Subtracts the Master Bias frame from a DET frame.

Parameters

det	DET frame to subtract
masterbias_frame	the Master bias frame
params	correct bias parameters

Returns: the error code

This function applies to the RI extensions, it is applied to frames in basic calibration recipes and to frames used in science reduction in stare mode. The Master Bias extensions are simply subtracted from the corresponding extensions in the input Frame, taking into account the associated Bad Pixel Map extensions. The output frame is an image with associated bad pixel map and statistical errors. The output bad pixel maps are the combination of the input ones.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the frame is not tagged has MASTER BIAS

Definition at line 86 of file moo_drl.c.

References MOO_BADPIX_GOOD, moo_det_create(), moo_det_delete(), moo_det_load_single(), moo_single_get_image(), moo_single_get_qual(), and MOO_TYPE_RI.

◆ moo_correct_dark()

cpl_error_code moo_correct_dark	(	moo_det *	det,
		moo_det *	detoff,
		const cpl_frame *	masterDarkVis,
		const cpl_frame *	masterDarkNir
	)

Subtracts the master dark frame from a frame after scaling for exposure time (RI). Subtract OFF frame from ON frame (YJ, H)

Parameters

det	DET structure to subtract
detoff	corresponding DET Off structure or NULL
masterDarkVis	Master dark frame for optical detectors
masterDarkNir	Master dark frame for IR detectors or NULL

Returns: the error code

The input frame is corrected for dark current using the Master Dark frame and accounting for its associated Bad Pixel Mask darkbpixmask which identifies pixels where the dark current is far above the average. In RI extensions the Master Dark is scaled according to the exposure time and subtracted from the input frame. The bad pixel masks are combined and propagated. In YJ and H extensions, the OFF frame or the master dark (IR) is subtracted from the ON frame and the bad pixel masks are combined and propagated.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the frame is not tagged has MASTER DARK_VIS

Definition at line 250 of file moo_drl.c.

References MOO_BADPIX_GOOD, moo_det_create(), moo_det_delete(), moo_det_get_single(), moo_det_load_single(), moo_detector_get_extname(), moo_pfits_get_exptime(), moo_single_get_image(), moo_single_sub(), MOO_TYPE_H, MOO_TYPE_RI, and MOO_TYPE_YJ.

◆ moo_correct_detlin()

cpl_error_code moo_correct_detlin	(	moo_det *	det,
		const cpl_frame *	cube_frame
	)

Apply the detector linearity correction.

Parameters

det	DET frame to correct
cube_frame	cube coefficients to appply linearity correction by pixel

Returns: the error code

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the frame of COEFF is invalid

Definition at line 507 of file moo_drl.c.

References MOO_BADPIX_GOOD, moo_cube_delete(), moo_det_get_primary_header(), moo_det_load_single(), and moo_qc_set_is_linearcor().

Referenced by moo_prepare().

◆ moo_correct_tell()

cpl_error_code moo_correct_tell	(	moo_rbn *	rbn,
		moo_telluric *	tell
	)

Apply the telluric correction to 1D rebinned spectra.

Parameters

rbn	RBN specta
tell	TELLURIC correction

Returns: Flux calibrated frame

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 124 of file moo_correct_tell.c.

References MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_pfits_get_cd1_1(), moo_pfits_get_crpix1(), moo_pfits_get_crval1(), moo_rbn_get_fibre_table(), moo_rbn_get_primary_header(), moo_rbn_load_single(), moo_rbn_single_get_header(), moo_rbn_single_get_image(), moo_telluric_get_band(), moo_telluric_get_image(), and moo_telluric_get_index().

◆ moo_correct_tell_science()

cpl_error_code moo_correct_tell_science	(	moo_sci *	sci,
		moo_telluric *	tell
	)

Apply the telluric correction to SCI.

Parameters

sci	sky Input wavelength calibrated, sky corrected frame
tell	telluric corerction

Returns: the error code

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 246 of file moo_correct_tell.c.

References MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_pfits_get_cd1_1(), moo_pfits_get_crpix1(), moo_pfits_get_crval1(), moo_sci_get_target_table(), moo_sci_load_single(), moo_sci_single_get_header(), moo_sci_single_get_image(), moo_telluric_get_band(), moo_telluric_get_image(), and moo_telluric_get_index().

◆ moo_create_s1d()

cpl_error_code moo_create_s1d	(	cpl_frame *	sci_frame,
		moo_create_s1d_params *	params,
		const char *	tag,
		moo_products *	products
	)

Apply the telluric correction to SCI.

Parameters

sci_frame	Input wavelength calibrated, sky corrected frame
params	Parameters od create_s1d
tag	The S1D associated tag
products	the saving products structure

Returns: the error code

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 177 of file moo_create_s1d.c.

References MOO_BADPIX_GOOD, moo_products_add_s1d(), moo_s1d_delete(), moo_s1d_save(), moo_sci_create(), moo_sci_delete(), moo_sci_get_single(), moo_sci_get_target_table(), moo_sci_load_single(), and moo_target_table_get_exptime().

◆ moo_extract()

moo_ext * moo_extract	(	moo_det *	det,
		moo_loc *	loc,
		moo_psf *	master_flat,
		moo_extract_params *	params,
		const char *	filename
	)

extract the 1D spectrum of fibres

Parameters

det	DET frame to extract
loc	LOC localisation of the fibres
master_flat	PSF the master flat or NULL
params	the extraction parameters
filename	the file name for the result

Returns: the EXT spectra

This function is to extract fibre spectra into 1D with two different methods defined by extract-method: “sum” or “optimal”. The latter will request the MasterFlat input, in order to use the fibre profiles along the slit.

Bad pixels flags:

BADPIX_OUTSIDE_DATA_RANGE

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the localisation fibres table is NULL

Definition at line 523 of file moo_extract.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_COSMETIC, MOO_BADPIX_GOOD, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_get_fibre_table(), moo_det_load_single(), moo_detector_get_extname(), moo_ext_add_fibre_table(), moo_ext_add_single(), moo_ext_delete(), moo_ext_new(), moo_fibres_table_add_extract_cols(), moo_fibres_table_by_index(), moo_fibres_table_get_spectro_indexext(), moo_fits_create(), moo_loc_get_fibre_table(), moo_loc_get_single(), and moo_psf_get_single().

◆ moo_flat_shift_compute()

cpl_error_code moo_flat_shift_compute	(	moo_det *	det,
		moo_loc *	ff_trace
	)

Compute the shift between FF_TRACE and FLAT.

Parameters

det	DET frame to analyse
ff_trace	the given FF_TRACE

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if DET has not a fibre table

Definition at line 174 of file moo_flat_shift_compute.c.

References MOO_BADPIX_COSMETIC, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), moo_detector_get_extname(), and moo_loc_get_single().

◆ moo_localise()

moo_loc * moo_localise	(	moo_det *	det,
		const cpl_frame *	guess_loc,
		moo_localise_params *	params,
		const char *	locname
	)

To localise the centroid of fibre spectrum on frames.

END CREATE_GUESS

Parameters

det	DET frame to localize
guess_loc	FF_TRACE_GUESS frame or NULL
params	the localisation parameters
locname	the file name of the result

Returns: the FF_TRACE or NULL in error case

This function is to find the localisation of the centroid of each fibre spectrum on CCD Frame, then generate the FF_TRACE. It is able be excuted in two cases:

construct the FF_TRACE from scratch
construct the FF_TRACE based on user input FF_TRACE_GUESS _Flags considered as bad :BADPIX_COSMETIC | BADPIX_HOT

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if DET has not a fibre table

Definition at line 3093 of file moo_localise.c.

References MOO_BADPIX_COSMETIC, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_loc_delete(), and moo_loc_load().

◆ moo_model_flat()

moo_psf * moo_model_flat	(	moo_det *	det,
		moo_loc *	loc,
		moo_model_flat_params *	params,
		const char *	filename
	)

To extract 2D FF and model it, resulting MASTER_FLAT.

Parameters

det	DET frame to extract
loc	LOC localisation of the fibres
params	the model flat parameters
filename	the name of the result

Returns: the PSF model flat

This function is to model the extracted FF, and resultsing a modelled FF, i.e., the MasterFlat.

_Flags considered as bad : BADPIX_COSMETIC | BADPIX_HOT

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the LOC file has not a fibre table

Definition at line 1546 of file moo_model_flat.c.

References MOO_BADPIX_COSMETIC, MOO_BADPIX_HOT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), moo_detector_get_extname(), moo_loc_get_fibre_table(), moo_loc_get_single(), moo_psf_add_single(), and moo_psf_create().

◆ moo_molecfit_calctrans()

moo_telluric * moo_molecfit_calctrans	(	const cpl_frame *	rbn_frame,
		const char *	modename,
		const cpl_frame *	molecules_frame,
		const cpl_frame *	atm_frame,
		const cpl_frame *	best_fit_frame,
		const cpl_frame *	kernel_lib_frame,
		moo_molecfit_calctrans_params *	params
	)

Apply the molcecfit calctrans to the RBN to compute telle telluric correction.

Parameters

rbn_frame	The RBN SPECTRA
modename	mode LR or HR
molecules_frame	The MOLECULES frame
atm_frame	the ATM frame (from model)
best_fit_frame	the BEST_FIT frame (from model)
kernel_lib_frame	the KERNEL frame
params	the calctrans parameters

Returns: Flux calibrated frame

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 1428 of file moo_molecfit.c.

References MOO_BADPIX_GOOD, moo_kernel_delete(), moo_kernel_get_header(), moo_kernel_get_matrix(), moo_kernel_load(), moo_molectable_delete(), moo_molectable_get_data(), moo_molectable_load(), moo_molectable_new(), moo_pfits_get_cd1_1(), moo_pfits_get_crpix1(), moo_pfits_get_crval1(), moo_rbn_create(), moo_rbn_delete(), moo_rbn_get_fibre_table(), moo_rbn_get_single(), moo_rbn_single_get_header(), moo_rbn_single_get_image(), moo_rbn_single_load(), MOO_TELLURIC_EXT_RI, moo_telluric_new(), and moo_telluric_set_image().

◆ moo_molecfit_model()

moo_molectable * moo_molecfit_model	(	const cpl_frame *	sci_frame,
		const char *	modename,
		const cpl_frame *	molecule_frame,
		const cpl_frame *	winc_frame,
		moo_molectable **	pmt_atm_fitted,
		moo_molectable **	best_fitted_model,
		moo_molecfit_model_params *	params
	)

Apply the relative flux calibration to 1D rebinned spectra.

Parameters

sci_frame	the sky Input wavelength calibrated, sky corrected frame
modename	the instrument mode (LR or HR)
molecule_frame	the MOLECULE frame
winc_frame	the WAVE_INCLUDE frame
pmt_atm_fitted	The ATM fitted result
best_fitted_model	The BEST FITTED model result
params	the molecfit model parameters

Returns: The best fitted parameters result

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 1158 of file moo_molecfit.c.

References MOO_BADPIX_GOOD, moo_detector_get_name(), moo_molectable_delete(), moo_molectable_get_data(), moo_molectable_load(), moo_molectable_new(), moo_molectable_set_data(), moo_pfits_get_cd1_1(), moo_pfits_get_crpix1(), moo_pfits_get_crval1(), moo_sci_create(), moo_sci_delete(), moo_sci_get_single(), moo_sci_single_get_header(), moo_sci_single_get_image(), and moo_sci_single_load().

◆ moo_prepare()

moo_det * moo_prepare	(	const cpl_frame *	rawframe,
		const char *const	badpixmask_rp,
		const char *const	badpixmask_nl,
		const cpl_frame *	masterbias,
		const cpl_frame *	cube_frame,
		moo_prepare_params *	params
	)

This function transforms RAW frames in DET frames attaching the default bad pixel map and an error image.

Parameters

rawframe	the RAW cpl frame to prepare
badpixmask_rp	the filename of the bad pixel mask RP or NULL
badpixmask_nl	the filename of the bad pixel mask NL or NULL
masterbias	the MASTER_BIAS frame or NULL if not
cube_frame	the LINEARITY_COEFF_CUBE frame or NULL if no correction
params	the prepare parameters

Returns: the DET corresponding to the given raw files

This function is placed at the beginning of every recipe, it transforms an input RAW frame in a DET frame attaching to it additional extensions: a bad pixel map, and an error image for each detector extension. The bad pixel map is the default one or a zero image if the default map does not exist. The error image is built summing the Read Out Noise and the shot noise.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if raw frame is not from GROUP RAW

Definition at line 324 of file moo_prepare.c.

References moo_correct_detlin(), moo_det_delete(), moo_det_get_single(), moo_det_save(), moo_detector_get_extname(), and moo_prepare_adu().

◆ moo_prepare_adu()

moo_det * moo_prepare_adu	(	const cpl_frame *	rawframe,
		const char *const	badpixmask_rp,
		moo_prepare_params *	params
	)

This function transforms RAW frames in DET ADU frames attaching the default bad pixel.

Parameters

rawframe	the RAW cpl frame to prepare
badpixmask_rp	the filename of the bad pixel mask RP or NULL
params	the prepare parameters

Returns: the DET corresponding to the given raw files

This function is placed at the beginning of every recipe, it transforms an input RAW frame in a DET frame attaching to it additional extensions: a bad pixel map, and an error image for each detector extension. The bad pixel map is the default one or a zero image if the default map does not exist. The error image is built summing the Read Out Noise and the shot noise.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if raw frame is not from GROUP RAW

Definition at line 430 of file moo_prepare.c.

References moo_det_create(), moo_det_delete(), moo_det_get_single(), moo_det_save(), moo_detector_get_extname(), moo_pfits_get_det_chip_live(), and moo_pfits_get_live().

Referenced by moo_prepare().

◆ moo_rebin()

moo_rbn * moo_rebin	(	moo_ext *	ext,
		moo_map *	wmap,
		moo_spectral_format *	sformat,
		moo_rebin_params *	params,
		const char *	filename
	)

Rebin an EXT spectra in RBN format.

Parameters

ext	EXT Extracted 1D spectra
wmap	EXT Wave map
sformat	the spectral format
params	the rebin parameters
filename	the file name for the result

Returns: the RBN spectra

This function rebin the extracted spectra.

Bad pixels flags:

BADPIX_OUTSIDE_DATA_RANGE

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 783 of file moo_rebin.c.

References MOO_BADPIX_GOOD, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_detector_get_name(), moo_ext_get_fibre_table(), moo_ext_load_single(), moo_fibres_table_add_rebin_cols(), moo_fibres_table_get_spectro_indexext(), moo_fits_create(), moo_rbn_add_fibre_table(), moo_rbn_add_single(), moo_rbn_delete(), moo_rbn_new(), moo_rbn_single_delete(), moo_rbn_single_get_data(), moo_rbn_single_get_errs(), moo_rbn_single_new(), moo_rbn_single_set_wcs1(), moo_spectral_format_get(), moo_spectral_format_get_wave_range(), moo_spectral_format_info_delete(), and moo_table_and_selected_sequal_string().

◆ moo_remove_CRH()

moo_det * moo_remove_CRH	(	moo_detlist *	detlist,
		moo_masklist *	cosmiclist,
		moo_crh_params *	params
	)

Remove CRH in single frames or in a combination of multiple frames.

Parameters

detlist	list of DET frames
cosmiclist	list of MASK or NULL
params	the remove CRH parameters

Returns: the DET result

The function will behave differently depending on the number of input frames. For now, only multiple input is implemented.

With, as input, a series of n (N = n ≥ 3) similar frames in DET format, the function uses the collapse functionalities from HDRL, specified by crh-method. The default value for crh-method will depend on the recipe: “median” in moons_mbias, “sigclip” in moons_mdark
_Flags considered as bad : BADPIX_COSMETIC

Bad pixels flags:

BADPIX_COSMIC_UNREMOVED is set in SIGCLIP mode

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if DET list size is lower or equal to zero

Definition at line 427 of file moo_remove_crh.c.

References MOO_BADPIX_GOOD, moo_det_delete(), moo_det_get_fibre_table(), moo_det_new(), moo_detlist_get(), moo_qc_set_ncom(), moo_qc_set_ncrh_tot(), MOO_TYPE_H, MOO_TYPE_RI, and MOO_TYPE_YJ.

◆ moo_reproject_model()

cpl_error_code moo_reproject_model	(	moo_det *	flat1,
		moo_loc *	loc1,
		moo_psf *	model_flat1,
		const char *	filename
	)

Reporject a model on detector.

Parameters

flat1	DET first flat field
loc1	LOC localisation of the first flat field
model_flat1	PSF model of the first flat field
filename	the name of the produce DET file

Returns: DET the pixel to pixel variation map

Definition at line 232 of file moo_compute_p2p.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_LOW_QE, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_det_load_single(), moo_fits_create(), moo_fits_write_extension_image(), moo_loc_get_fibre_table(), moo_loc_get_single(), and moo_psf_get_single().

◆ moo_select_sky()

cpl_array * moo_select_sky	(	const char *	targname,
		int	indextarg,
		int	obj_index,
		double	obj_targalpha,
		double	obj_targdelta,
		cpl_table *	target_table,
		const char *	index_colname,
		cpl_table *	sky_stare_table,
		moo_detector_type	type,
		int	maxdistslit,
		double	mintrans,
		int	min_sky,
		double	radius,
		double	step_r,
		int	target_table_idx,
		moo_f2f *	f2f,
		cpl_array *	allsky_indexes
	)

This function selects sky fibres around a target object.

Parameters

targname	Name of the target object
indextarg	Index of the target in the TARGET_TABLE
obj_index	Index RBN of the target in the TARGET_TABLE
obj_targalpha	Alpha position of the target
obj_targdelta	Delta position of the target
target_table	the TARGET TABLE
index_colname	the name of the INDEX column in table
sky_stare_table	the SKY fibres results table
type	the detector type RI,YJ or H
maxdistslit	the maximum distance on the slit for the sky fibres
mintrans	the minimum value of transmission for the sky fibres
min_sky	the minimum of sky fibres to find
radius	the radius around the object position to find the sky fibres
step_r	the step to increase rhe radius to search the sky fibres
f2f	the fibre to fibre transmission
allsky_indexes	the indexes of sky fibres in target_table

Returns

the selected sky indexes

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 122 of file moo_sub_sky_stare.c.

References moo_f2f_get_trans_colname(), moo_select_sky(), and moo_sky_distance().

Referenced by moo_select_sky().

◆ moo_single_compute_noise_map()

cpl_error_code moo_single_compute_noise_map	(	moo_single *	single,
		moo_nos_params *	params,
		cpl_imagelist *	list,
		cpl_imagelist *	qlist
	)

Calculates the noisey bad pixel mask for one extension.

Parameters

single	DET single extension
params	noise map parameters
list	DARK list DATA images
qlist	DARK list QUAL images

Returns: the error code

Bad pixels flags:

BADPIX_NOISY

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 559 of file moo_drl.c.

References MOO_BADPIX_NOISY, moo_compute_sigma_map(), moo_kappa_sigma_clipping(), moo_single_apply_mask(), and moo_single_get_data().

Referenced by moo_compute_noise_map().

◆ moo_sub_sky_stare()

moo_sci * moo_sub_sky_stare	(	moo_rbn *	obja_rbn,
		moo_target_table *	target_table,
		moo_rbn *	objb_rbn,
		moo_f2f *	f2f,
		const cpl_frame *	solflux_frame,
		const cpl_frame *	airglow_group_frame,
		const cpl_frame *	airglow_var_frame,
		moo_sub_sky_stare_params *	params,
		const char *	filename,
		int	ispaired
	)

This function subtracts the sky in wavelength calibrated and extracted science frames obtain in Stare mode observations.

Parameters

obja_rbn	RBN Wavelength calibrated science spectra for object A
target_table	TARGET_TABLE Attached target table
objb_rbn	RBN Wavelength calibrated science spectra for object B
f2f	the F2F (fibre to fibre transmission) table
solflux_frame	the monthly averages of solar radio flux at 10.7 cm frame
airglow_group_frame	the airglow line list frame (use in subsky)
airglow_var_frame	the airglow scaling parameters frame (use in subsky)
params	the sub sky stare parameters
filename	the name of the result SCI
ispaired	MOO_SCI1D_NOT_PAIRED or MOO_SCI1D_PAIRED

Returns: the SCI result

_Flags considered as bad : BADPIX_COSMETIC | BADPIX_HOT

Bad pixels flags:

BADPIX_COSMIC_UNREMOVED is set in SIGCLIP mode

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 810 of file moo_sub_sky_stare.c.

References MOO_BADPIX_CALIB_DEFECT, MOO_BADPIX_OUTSIDE_DATA_RANGE, moo_f2f_order_by_indexrbn(), moo_fits_create(), moo_pfits_get_dit(), moo_pfits_get_exptime(), moo_pfits_get_ndit(), moo_rbn_get_fibre_table(), moo_rbn_get_single(), moo_rbn_load_single(), moo_rbn_single_get_header(), moo_sci_add_single(), moo_sci_add_target_table(), moo_sci_delete(), moo_sci_new(), moo_target_table_duplicate(), moo_target_table_select_obj_index(), moo_target_table_select_sky_index(), and moo_target_table_xswitch_paired().

Referenced by moo_combine_pair().

◆ moo_subtract_nod()

moo_det * moo_subtract_nod	(	moo_det *	object,
		moo_det *	sky,
		const char *	filename
	)

Sky from object subtraction.

Parameters

object	[DET] object det file
sky	[DET] skt det file
filename	file name of the new nod DET

Returns: object-sky [DET]

_Flags considered as bad :

Bad pixels flags:

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL
CPL_ERROR_ILLEGAL_INPUT if the SCI list have a size

Definition at line 70 of file moo_subtract_nod.c.

References MOO_BADPIX_GOOD, moo_det_create(), moo_det_delete(), moo_det_get_fibre_table(), moo_det_get_primary_header(), moo_det_load(), moo_det_rescale_using_exptime(), moo_det_save(), moo_det_subtract(), moo_fibres_table_add_nod_cols(), and moo_qc_set_frame_raw2().

◆ moo_wavesol()

moo_map * moo_wavesol	(	moo_ext *	arc_ext,
		const char *	lineCatname,
		moo_spectral_format *	sformat,
		moo_loc *	loc,
		moo_map *	wmap,
		moo_wavesol_params *	params
	)

Computes the wavelength solution from 1D extracted arc spectra.

Parameters

arc_ext	EXT Extracted 1D arc spectra
lineCatname	Name of the Line list file
sformat	the SPECTRAL FORMAT
loc	LOC localization trace
wmap	the WAVE MAP GUESS if a preliminary solution is alrezady computed
params	the wavesol parameters

Returns: the EXT spectra

This function computes the wavelength solution. It first determine the (X,Y) positions of a set of arc lines given as input, and then creates a wavelength map for each detector extensions in the input frame.

Bad pixels flags:

None

Error code:

CPL_ERROR_NULL_INPUT if an input pointer is NULL

Definition at line 2728 of file moo_wavesol.c.

References moo_map_check().

Functions

Detailed Description

Function Documentation

◆ moo_apply_flat()

◆ moo_apply_p2p()

◆ moo_calib_flux()

◆ moo_coadd()

◆ moo_combine_pair()

◆ moo_combine_sky()

◆ moo_compute_fibtrans()

◆ moo_compute_hot_map()

◆ moo_compute_noise_map()

◆ moo_compute_p2p()

◆ moo_compute_resp()

◆ moo_compute_slitoffset()

◆ moo_correct_bias()

◆ moo_correct_dark()

◆ moo_correct_detlin()

◆ moo_correct_tell()

◆ moo_correct_tell_science()

◆ moo_create_s1d()

◆ moo_extract()

◆ moo_flat_shift_compute()

◆ moo_localise()

◆ moo_model_flat()

◆ moo_molecfit_calctrans()

◆ moo_molecfit_model()

◆ moo_prepare()

◆ moo_prepare_adu()

◆ moo_rebin()

◆ moo_remove_CRH()

◆ moo_reproject_model()

◆ moo_select_sky()

◆ moo_single_compute_noise_map()

◆ moo_sub_sky_stare()

◆ moo_subtract_nod()

◆ moo_wavesol()