xsh_utils_ifu.c File Reference

#include <math.h>
#include <string.h>
#include <xsh_error.h>
#include <xsh_utils_ifu.h>
#include <xsh_utils_image.h>
#include <xsh_utils_imagelist.h>
#include <xsh_utils_wrappers.h>
#include <xsh_utils_table.h>
#include <xsh_pfits.h>
#include <xsh_model_io.h>
#include <xsh_data_rec.h>
#include <xsh_data_spectrum.h>
#include <xsh_dfs.h>
#include <xsh_drl.h>
#include <xsh_globals.h>

Go to the source code of this file.

Macros
#define	PI_NUMB   (3.1415926535897932384626433832795)

Functions
static double	xsh_interpol (double x, double x1, double x2, double y1, double y2)
static void	xsh_plist_set_coord1 (cpl_propertylist **plist, const double crpix1, const double crval1, const double cdelt1)
	set world coordinate system
static void	xsh_plist_set_coord2 (cpl_propertylist **plist, const double crpix2, const double crval2, const double cdelt2)
	set world coordinate system
static void	xsh_plist_set_coord3 (cpl_propertylist **plist, const int crpix3, const double crval3, const double cdelt3)
	set world coordinate system
static void	xsh_plist_set_cd_matrix2 (cpl_propertylist **plist, const double cd1_1, const double cd1_2, const double cd2_1, const double cd2_2)
	set world coordinate system: CD matrix
static void	xsh_plist_set_cd_matrix3 (cpl_propertylist **plist, const double cd1_3, const double cd2_3, const double cd3_1, const double cd3_2, const double cd3_3)
	set world coordinate system: CD matrix
xsh_change_plist_cube
set world coordinate system for a cube Parameters plist input propertylist name file name cenLambda central wawelength dispersion dispersion cenpix central pixel center_x center x center_y center y
cpl_error_code	xsh_cube_set_wcs (cpl_propertylist *plist, float cenLambda, float disp_x, float disp_y, float disp_z, float center_x, float center_y, int center_z)
void	xsh_edge_check (const int px, const int nx, const int rad_x, int *llx, int *urx)
	check edge values (llx,urx) fit in image size (1,nx)
void	xsh_convert_xy_to_ws (double x_centroid, double *p_obj_cen, double *p_slit, double *p_wave, const int lly, const int nx, const int row, double *p_obj_cen_s, double *p_obj_cen_w)
	convert X-Y coordinates to Wavelengt Slit space
cpl_error_code	xsh_table_edges_swap_low_upp (cpl_table **tab)
	swap lower and upper edge columns
cpl_table *	xsh_table_edge_prepare (const char *name)
	Add to edges table columns to store LOW/CEN/UPP object positions.
cpl_error_code	xsh_ifu_trace_object_calibrate (const char *ifu_object_ff_name, const char *order_tab_edges_ifu_name, const char *slit_map_name, const char *wave_map_name)
	Function to calibrate object traces in IFU mode.
cpl_error_code	xsh_frame_check_model_cfg_is_proper_for_sci (cpl_frame *model_config_frame, cpl_frame *sci_frame, xsh_instrument *instrument)
	Check if a model configuration frame has been corrected for flexures.
cpl_error_code	xsh_frame_check_model_cfg_is_afc_corrected (cpl_frame *model_config_frame)
	utility to check if a frame has been corrected for flexures
static cpl_error_code	xsh_add_correct_coeff (cpl_table **table, cpl_propertylist *plist, const char *prefix, const int row, const char *col12, const char *col32)
static cpl_frame *	xsh_crea_correct_coeff (cpl_frame *qc_trace_merged_frame, xsh_instrument *inst)
static cpl_frame *	xsh_frame_build_sky_area (cpl_frame *slitmap_frame, const char *tag)
static cpl_frame *	xsh_frame_build_sky_map (cpl_frame *slitmap_frame, const double value, const char *tag)
cpl_frame *	xsh_build_ifu_map (cpl_frame *div_frame, cpl_frame *wavemap_frame, cpl_frame *slitmap_frame, xsh_instrument *instrument)
	Reconstruct IFU cube.
static cpl_error_code	xsh_monitor_spectrum3D_flux_qc (cpl_imagelist *data, cpl_imagelist *errs, cpl_imagelist *qual, cpl_propertylist *phead, const double wave_s, const double wave_e, const int index)
static cpl_error_code	xsh_monitor_spectrum3D_flux (cpl_imagelist *data, cpl_imagelist *errs, cpl_imagelist *qual, xsh_instrument *instrument, cpl_propertylist *phead)
	Computes flux, err, SNR on IFU cube over full range and sub intervals.
cpl_error_code	xsh_build_ifu_cube (cpl_frame *div_frame, cpl_frame *ifu_cfg_tab_frame, cpl_frame *ifu_cfg_cor_frame, cpl_frame *spectral_format_frame, cpl_frame *model_config_frame, cpl_frame *wavesol_frame, xsh_instrument *instrument, cpl_frameset *frameset, cpl_parameterlist *parameters, xsh_rectify_param *rectify_par, const char *recipe_id, const char *rec_prefix, const int frame_is_object)
	Reconstruct IFU cube.
cpl_matrix *	xsh_atrous (cpl_vector *spec, int nscales)
	Do a wavelet decomposition using atrous from IDL.
cpl_frameset *	xsh_shift_offsettab (cpl_frameset *shiftifu_frameset, double offset_low, double offset_up)
	Do a wavelet decomposition using atrous from IDL.

Macro Definition Documentation

PI_NUMB

#define PI_NUMB   (3.1415926535897932384626433832795)

Definition at line 46 of file xsh_utils_ifu.c.

Function Documentation

xsh_add_correct_coeff()

static cpl_error_code xsh_add_correct_coeff ( cpl_table **  table, cpl_propertylist *  plist, const char *  prefix, const int  row, const char *  col12, const char *  col32  )

static

Definition at line 1077 of file xsh_utils_ifu.c.

References check.

Referenced by xsh_crea_correct_coeff().

xsh_atrous()

cpl_matrix * xsh_atrous	(	cpl_vector *	spec,
		int	nscales
	)

Do a wavelet decomposition using atrous from IDL.

Parameters

[in]	spec	spectrum
[in]	nscales	number os scales

Returns

matrix of wavelet decomposition

Definition at line 2379 of file xsh_utils_ifu.c.

References check, filter, smooth(), XSH_ASSURE_NOT_ILLEGAL, XSH_ASSURE_NOT_NULL, XSH_CALLOC, XSH_FREE, xsh_free_matrix(), xsh_free_vector(), xsh_msg_dbg_medium, and xsh_unwrap_vector().

Referenced by main(), and xsh_localize_ifu_slitlet().

xsh_build_ifu_cube()

cpl_error_code xsh_build_ifu_cube	(	cpl_frame *	div_frame,
		cpl_frame *	ifu_cfg_tab_frame,
		cpl_frame *	ifu_cfg_cor_frame,
		cpl_frame *	spectral_format_frame,
		cpl_frame *	model_config_frame,
		cpl_frame *	wavesol_frame,
		xsh_instrument *	instrument,
		cpl_frameset *	frameset,
		cpl_parameterlist *	parameters,
		xsh_rectify_param *	rectify_par,
		const char *	recipe_id,
		const char *	rec_prefix,
		const int	frame_is_object
	)

Reconstruct IFU cube.

Parameters

[in]	div_frame	input frame flat field corrected
[in]	ifu_cfg_tab_frame	IFU configuration frame
[in]	ifu_cfg_cor_frame	IFU configuration frame
[in]	spectral_format_frame	spectral format frame
[in]	model_config_frame	model configuration frame
[in]	wavesol_frame	wavelength solution frame
[in]	instrument	instrument (arm) setting
[in]	frameset	input frame set
[in]	parameters	input parameter list
[in]	rectify_par	input parameters to specify rectification
[in]	recipe_id	input recipe id
[in]	rec_prefix	input recipe prefix
[in]	frame_is_object	flag to specify if input frame is object or sky

Returns

corrected table

Definition at line 1523 of file xsh_utils_ifu.c.

References xsh_instrument::arm, binx, biny, check, xsh_instrument::decode_bp, instrument, xsh_rectify_param::kernel_type, method, nx, ny, QFLAG_MISSING_DATA, xsh_rectify_param::rectif_bin_lambda, xsh_rectify_param::rectif_bin_space, xsh_rectify_param::rectif_radius, s, x, xsh_add_product_imagelist(), xsh_add_product_table(), xsh_add_temporary_file(), XSH_ARM_NIR, xsh_arm_tostring(), XSH_ARM_UVB, XSH_ARM_VIS, xsh_crea_correct_coeff(), xsh_cube_qc_trace_window(), xsh_cube_set_wcs(), xsh_frame_product(), xsh_free_frame(), xsh_free_image(), xsh_free_imagelist(), xsh_free_propertylist(), xsh_free_table(), xsh_free_vector(), xsh_imagelist_cut_dichroic_uvb(), xsh_iml_merge_wgt(), xsh_model_binxy(), xsh_model_config_load_best(), xsh_model_get_xy(), xsh_monitor_spectrum3D_flux(), xsh_msg, xsh_msg_debug, xsh_parameters_cut_uvb_spectrum_get(), xsh_pfits_get_binx(), xsh_pfits_get_biny(), xsh_pfits_set_extname(), xsh_pfits_set_pcatg(), xsh_plist_set_extra_keys(), XSH_PRE_DATA_TYPE, XSH_PRE_ERRS_TYPE, XSH_PRE_QUAL_TYPE, xsh_rec_list_create(), xsh_rec_list_free(), XSH_SPECTRUM_DATA_BPP, XSH_SPECTRUM_ERRS_BPP, XSH_SPECTRUM_QUAL_BPP, xsh_wavesol_eval_polx(), xsh_wavesol_eval_poly(), xsh_wavesol_load(), and y.

Referenced by xsh_scired_ifu_offset(), and xsh_scired_ifu_stare().

xsh_build_ifu_map()

cpl_frame * xsh_build_ifu_map	(	cpl_frame *	div_frame,
		cpl_frame *	wavemap_frame,
		cpl_frame *	slitmap_frame,
		xsh_instrument *	instrument
	)

Reconstruct IFU cube.

Parameters

[in]	div_frame	input frame flat field corrected
[in]	wavemap_frame	slit map frame
[in]	slitmap_frame	wave map frame
[in]	model_config_frame	model configuration frame
[in]	instrument	instrument (arm) setting

Returns

corrected table

Definition at line 1248 of file xsh_utils_ifu.c.

References check, instrument, xsh_add_temporary_file(), xsh_frame_build_sky_area(), xsh_frame_build_sky_map(), xsh_frame_image_save2ext(), xsh_frame_product(), xsh_free_image(), xsh_free_propertylist(), xsh_hms2deg(), XSH_IFU_MAP_SKY, xsh_instrument_arm_tostring(), xsh_pfits_get_tel_targ_alpha(), xsh_pfits_get_tel_targ_delta(), and xsh_sess2deg().

Referenced by xsh_scired_ifu_offset(), and xsh_scired_ifu_stare().

xsh_convert_xy_to_ws()

void xsh_convert_xy_to_ws	(	double	x_centroid,
		double *	p_obj_cen,
		double *	p_slit,
		double *	p_wave,
		const int	lly,
		const int	nx,
		const int	row,
		double *	p_obj_cen_s,
		double *	p_obj_cen_w
	)

convert X-Y coordinates to Wavelengt Slit space

Parameters

x_centroid	centrod position on X axis
p_obj_cen	[IN] pointer to central object array
p_slit	[IN] pointer to slit array
p_wave	[IN] pointer to wave array
lly	[IN] Lower left X
nx	[IN] number of X points (vector size) l
row	[IN] detector row position(Y)
p_obj_cen_s	[OUT] pointer to object s position
p_obj_cen_w	[OUT] pointer to object s position

Returns

void

Definition at line 460 of file xsh_utils_ifu.c.

References lly, nx, and xsh_interpol().

Referenced by xsh_ifu_trace_object_calibrate().

xsh_crea_correct_coeff()

static cpl_frame * xsh_crea_correct_coeff ( cpl_frame *  qc_trace_merged_frame, xsh_instrument *  inst  )

static

Definition at line 1110 of file xsh_utils_ifu.c.

References check, xsh_add_correct_coeff(), xsh_frame_product(), xsh_free_propertylist(), xsh_free_table(), xsh_instrument_arm_tostring(), xsh_msg, XSH_QC_TRACE_FIT_C0, XSH_QC_TRACE_FIT_C1, and XSH_QC_TRACE_FIT_C2.

Referenced by xsh_build_ifu_cube().

xsh_cube_set_wcs()

cpl_error_code xsh_cube_set_wcs	(	cpl_propertylist *	plist,
		float	cenLambda,
		float	disp_x,
		float	disp_y,
		float	disp_z,
		float	center_x,
		float	center_y,
		int	center_z
	)

Definition at line 331 of file xsh_utils_ifu.c.

References PI_NUMB, xsh_hms2deg(), xsh_pfits_get_dec(), xsh_pfits_get_posangle(), xsh_pfits_get_ra(), xsh_pfits_get_tel_targ_alpha(), xsh_pfits_get_tel_targ_delta(), xsh_plist_set_cd_matrix2(), xsh_plist_set_cd_matrix3(), xsh_plist_set_coord1(), xsh_plist_set_coord2(), xsh_plist_set_coord3(), and xsh_sess2deg().

Referenced by xsh_build_ifu_cube().

xsh_edge_check()

void xsh_edge_check	(	const int	px,
		const int	nx,
		const int	rad_x,
		int *	llx,
		int *	urx
	)

check edge values (llx,urx) fit in image size (1,nx)

Parameters

px	[IN] point position
nx	[IN] x image size
rad_x	[IN] x radii
llx	[OUT] lower left X
urx	[OUT] upper right X

Returns

void

Definition at line 428 of file xsh_utils_ifu.c.

References llx, nx, and urx.

Referenced by xsh_ifu_trace_object_calibrate().

xsh_frame_build_sky_area()

static cpl_frame * xsh_frame_build_sky_area ( cpl_frame *  slitmap_frame, const char *  tag  )

static

Definition at line 1155 of file xsh_utils_ifu.c.

References check, xsh_free_image(), xsh_free_propertylist(), and XSH_PRE_DATA_BPP.

Referenced by xsh_build_ifu_map().

xsh_frame_build_sky_map()

static cpl_frame * xsh_frame_build_sky_map ( cpl_frame *  slitmap_frame, const double  value, const char *  tag  )

static

Definition at line 1206 of file xsh_utils_ifu.c.

References check, xsh_add_temporary_file(), xsh_free_image(), xsh_free_propertylist(), XSH_PRE_DATA_BPP, and XSH_PRE_DATA_TYPE.

Referenced by xsh_build_ifu_map().

xsh_frame_check_model_cfg_is_afc_corrected()

cpl_error_code xsh_frame_check_model_cfg_is_afc_corrected

(

cpl_frame *

model_config_frame

)

utility to check if a frame has been corrected for flexures

Parameters

model_config_frame

input frame

Returns

corrected table

Definition at line 1053 of file xsh_utils_ifu.c.

References check, xsh_free_propertylist(), xsh_msg_error, and xsh_pfits_get_raw1catg().

Referenced by xsh_check_afc(), and xsh_scired_ifu_stare().

xsh_frame_check_model_cfg_is_proper_for_sci()

cpl_error_code xsh_frame_check_model_cfg_is_proper_for_sci	(	cpl_frame *	model_config_frame,
		cpl_frame *	sci_frame,
		xsh_instrument *	instrument
	)

Check if a model configuration frame has been corrected for flexures.

Parameters

model_config_frame	model configuration frame
sci_frame	science frame
instrument	instrument setting

Returns

cpl error code

Definition at line 984 of file xsh_utils_ifu.c.

References check, instrument, xsh_free_propertylist(), xsh_msg_error, xsh_pfits_get_obs_id(), xsh_pfits_get_obs_targ_name(), and xsh_pfits_get_slit_value().

Referenced by xsh_check_afc(), and xsh_scired_ifu_stare().

xsh_ifu_trace_object_calibrate()

cpl_error_code xsh_ifu_trace_object_calibrate	(	const char *	ifu_object_ff_name,
		const char *	order_tab_edges_ifu_name,
		const char *	slit_map_name,
		const char *	wave_map_name
	)

Function to calibrate object traces in IFU mode.

Parameters

ifu_object_ff_name	name of input object frame (flat field corrected)
order_tab_edges_ifu_name	name of input edge order table
slit_map_name	slit map filename
wave_map_name	wave map filename

Returns

cpl error code

Definition at line 701 of file xsh_utils_ifu.c.

References biny, check, llx, lly, nx, ny, urx, ury, XSH_ARM_NIR, xsh_arm_tostring(), XSH_ARM_UNDEFINED, XSH_ARM_UVB, XSH_ARM_VIS, xsh_convert_xy_to_ws(), xsh_edge_check(), xsh_free_image(), xsh_free_propertylist(), xsh_image_fit_gaussian_max_pos_x_window(), xsh_msg, xsh_pfits_get_biny(), xsh_pfits_get_pcatg(), xsh_pfits_set_pcatg(), xsh_table_edge_prepare(), and xsh_table_edges_swap_low_upp().

Referenced by xsh_scired_ifu_stare().

xsh_interpol()

static double xsh_interpol ( double  x, double  x1, double  x2, double  y1, double  y2  )

static

Definition at line 49 of file xsh_utils_ifu.c.

References x.

Referenced by xsh_convert_xy_to_ws().

xsh_monitor_spectrum3D_flux()

static cpl_error_code xsh_monitor_spectrum3D_flux ( cpl_imagelist *  data, cpl_imagelist *  errs, cpl_imagelist *  qual, xsh_instrument *  instrument, cpl_propertylist *  phead  )

static

Computes flux, err, SNR on IFU cube over full range and sub intervals.

Parameters

[in]	data	cube
[in]	errs	cube
[in]	qual	cube
[in]	instrument	to specify detector's arm
	[in/out]	phead primary header to be updated

Note

wavelength is expected to increase along the cube Z axis

Returns

cpl_error_code

Definition at line 1458 of file xsh_utils_ifu.c.

References check, instrument, XSH_ARM_NIR, XSH_ARM_UVB, XSH_ARM_VIS, xsh_instrument_get_arm(), and xsh_monitor_spectrum3D_flux_qc().

Referenced by xsh_build_ifu_cube().

xsh_monitor_spectrum3D_flux_qc()

static cpl_error_code xsh_monitor_spectrum3D_flux_qc ( cpl_imagelist *  data, cpl_imagelist *  errs, cpl_imagelist *  qual, cpl_propertylist *  phead, const double  wave_s, const double  wave_e, const int  index  )

static

Definition at line 1335 of file xsh_utils_ifu.c.

References check, xsh_free_image(), xsh_free_imagelist(), xsh_pfits_get_cdelt3(), xsh_pfits_get_crval3(), and XSH_QC_FLUX.

Referenced by xsh_monitor_spectrum3D_flux().

xsh_plist_set_cd_matrix2()

static void xsh_plist_set_cd_matrix2 ( cpl_propertylist **  plist, const double  cd1_1, const double  cd1_2, const double  cd2_1, const double  cd2_2  )

static

set world coordinate system: CD matrix

Parameters

plist	input propertylist
cd1_1	value of CD1_1
cd1_2	value of CD1_2
cd2_1	value of CD2_1
cd2_2	value of CD2_2

Returns

updated propertylist

Definition at line 220 of file xsh_utils_ifu.c.

References check.

Referenced by xsh_cube_set_wcs().

xsh_plist_set_cd_matrix3()

static void xsh_plist_set_cd_matrix3 ( cpl_propertylist **  plist, const double  cd1_3, const double  cd2_3, const double  cd3_1, const double  cd3_2, const double  cd3_3  )

static

set world coordinate system: CD matrix

Parameters

plist	input propertylist
cd1_3	value of CD1_3
cd2_3	value of CD2_3
cd3_1	value of CD3_1
cd3_2	value of CD3_2
cd3_3	value of CD3_3

Returns

updated propertylist

Definition at line 271 of file xsh_utils_ifu.c.

References check.

Referenced by xsh_cube_set_wcs().

xsh_plist_set_coord1()

static void xsh_plist_set_coord1 ( cpl_propertylist **  plist, const double  crpix1, const double  crval1, const double  cdelt1  )

static

set world coordinate system

Parameters

plist	input propertylist
crpix1	value of CRPIX1 (ref pixel axis 1 coord in pix coordinates)
crval1	value of CRVAL1 (ref pixel axis 1 coord in sky coordinates)
cdelt1	value of CDELT1 (ref pixel axis 1 size )

Returns

updated propertylist

Definition at line 99 of file xsh_utils_ifu.c.

Referenced by xsh_cube_set_wcs().

xsh_plist_set_coord2()

static void xsh_plist_set_coord2 ( cpl_propertylist **  plist, const double  crpix2, const double  crval2, const double  cdelt2  )

static

set world coordinate system

Parameters

plist	input propertylist
crpix2	value of CRPIX2 (ref pixel axis 2 coord in pix coordinates)
crval2	value of CRVAL2 (ref pixel axis 2 coord in sky coordinates)
cdelt2	value of CDELT2 (ref pixel axis 2 size )

Returns

updated propertylist

Definition at line 136 of file xsh_utils_ifu.c.

Referenced by xsh_cube_set_wcs().

xsh_plist_set_coord3()

static void xsh_plist_set_coord3 ( cpl_propertylist **  plist, const int  crpix3, const double  crval3, const double  cdelt3  )

static

set world coordinate system

Parameters

plist	input propertylist
crpix3	value of CRPIX3 (ref pixel axis 3 coord in pix coordinates)
crval3	value of CRVAL3 (ref pixel axis 3 coord in sky coordinates)
cdelt3	value of CDELT3 (ref pixel axis 3 size )

Returns

updated propertylist

Definition at line 175 of file xsh_utils_ifu.c.

Referenced by xsh_cube_set_wcs().

xsh_shift_offsettab()

cpl_frameset * xsh_shift_offsettab	(	cpl_frameset *	shiftifu_frameset,
		double	offset_low,
		double	offset_up
	)

Do a wavelet decomposition using atrous from IDL.

Parameters

[in]	spec	spectrum
[in]	nscales	number os scales

Returns

matrix of wavelet decomposition

Definition at line 2467 of file xsh_utils_ifu.c.

References check, size, xsh_frame_product(), xsh_free_frameset(), xsh_free_propertylist(), xsh_msg, XSH_SHIFTIFU_COLNAME_SHIFTSLIT, XSH_TABLE_FREE, and XSH_TABLE_LOAD.

Referenced by xsh_scired_ifu_offset(), and xsh_scired_ifu_stare().

xsh_table_edge_prepare()

cpl_table * xsh_table_edge_prepare

(

const char *

name

)

Add to edges table columns to store LOW/CEN/UPP object positions.

Parameters

name	[IN] input file name

Returns

corrected table

Definition at line 547 of file xsh_utils_ifu.c.

References check.

Referenced by xsh_ifu_trace_object_calibrate().

xsh_table_edges_swap_low_upp()

cpl_error_code xsh_table_edges_swap_low_upp

(

cpl_table **

tab

)

swap lower and upper edge columns

Parameters

tab	[INOUT] pointer to input/output table

Returns

if no error, CPL_ERROR_NONE

Definition at line 504 of file xsh_utils_ifu.c.

Referenced by xsh_ifu_trace_object_calibrate().