#include <math.h>
#include <hdrl.h>
#include <cpl.h>
#include <gsl/gsl_bspline.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_statistics_double.h>
#include <gsl/gsl_multifit.h>
#include <xsh_drl.h>
#include <xsh_drl_check.h>
#include <xsh_badpixelmap.h>
#include <xsh_data_pre.h>
#include <xsh_data_order.h>
#include <xsh_data_wavemap.h>
#include <xsh_data_localization.h>
#include <xsh_data_rec.h>
#include <xsh_dfs.h>
#include <xsh_pfits.h>
#include <xsh_error.h>
#include <xsh_utils.h>
#include <xsh_utils_image.h>
#include <xsh_utils_table.h>
#include <xsh_msg.h>
#include <xsh_fit.h>
#include <xsh_model_r250.h>
#include <xsh_efficiency_response.h>

Macros
#define	HAVE_INLINE 1

#define	REGDEBUG_MEDIAN_SPLINE 0

#define	REGDEBUG_BSPLINE 0

Functions
static xsh_wavemap_list *	xsh_wavemap_list_new (cpl_frame wavemap_frame, cpl_frame slitmap_frame, xsh_localization list, cpl_frame order_table_frame, xsh_pre pre_sci, int nbkpts, cpl_frame usr_def_sampl_points, cpl_frame ref_sky_list, cpl_frame sky_orders_chunks, xsh_subtract_sky_single_param sky_par, xsh_instrument instrument)

static xsh_rec_list *	xsh_wavemap_list_build_sky (xsh_wavemap_list wave_list, xsh_instrument instr)
	Build the sky spectrum list.

static int	xsh_wave_compare (const void un, const void deux)

static cpl_frame *	xsh_wavelist_subtract_sky (xsh_pre pre_sci, xsh_rec_list sky_list, xsh_wavemap_list wave_list, xsh_instrument instrument, const char rec_prefix, xsh_subtract_sky_single_param sky_par)
	subtract sky

static cpl_table *	xsh_table_unique_wave (cpl_table tab, const char wname, const char *fname)

static cpl_table *	xsh_model_to_table (const xsh_wavemap_list *wlist, const int order)
	determines sky outliers on a 1D spectrum via kappa-sigma clipping

static cpl_error_code	xsh_table_column_smooth (cpl_table *tab, const char name_i, const char *name_o, const int hsize)
	determines sky outliers on a 1D spectrum via kappa-sigma clipping

static cpl_error_code	xsh_table_column_clip (cpl_table *tab, const char name_d, const char *name_s, const double kappa, const int niter, const double gain, const double ron2, const int decode_bp)

static cpl_table *	xsh_detect_raw_data_outliers_1d (const xsh_wavemap_list *wlist, const int hsize, const double ron2, const double gain, const int order, const int iter, const int decode_bp)
	determines sky outliers on a 1D spectrum via kappa-sigma clipping

static cpl_table *	xsh_detect_raw_data_outliers_1d_slice (const xsh_wavemap_list *wlist, const int hsize, const double ron2, const double gain, const int order, const int iter, const int decode_bp, const double s1, const double s2, const int slice_id)
	determines sky outliers on a 1D spectrum via kappa-sigma clipping

static int	xsh_get_edge_x_min (xsh_order_list *otab, const int iorder, const int iy)

static int	xsh_get_edge_x_max (xsh_order_list *otab, const int iorder, const int iy)

static void	xsh_dump_table_on_region_file (cpl_table tab, const char fname, const int symbol)

static cpl_table *	xsh_create_sampl_table (const int iorder, double wave_ref, const int nref, xsh_wavemap_list wlist, const int nsampl_2, const char *prefix)

static cpl_table *	xsh_create_sampl_uniform_continuum (const int iorder, xsh_wavemap_list wlist, const int nsampl, const char prefix)

static cpl_error_code	xsh_wavemap_list_rms_sky_image_save (xsh_wavemap_list smap, const double ron2, const double gain, xsh_instrument instr, const int iter)

static double	xsh_skycorr_rms (xsh_wavemap_list *wlist, const int iorder, const double ron2, const double gain)

static cpl_table *	xsh_table_unique_column (cpl_table tab_inp, const char col_wav)

static cpl_table *	xsh_skycorr_sample_continuum (xsh_wavemap_list *wlist, const int ord, const int n)

static cpl_table *	xsh_skycorr_sampl_lines_from_static_tab (xsh_wavemap_list wlist, const cpl_table tab_ord, const int ord)

static cpl_table *	xsh_model2tab (xsh_wavemap_list *wlist, int order)

static cpl_table *	xsh_skycorr_wave_sampling_create (xsh_wavemap_list wlist, const int ord, const int nbkpts_ord, const cpl_table bkpts_tab)

static cpl_table *	xsh_detect_outliers_thres_new (xsh_wavemap_list wlist, const double kappa2, const double ron2, const double gain, const int order, const int iter, cpl_table *tab_line_res)

static cpl_error_code	xsh_model_fill_fit (xsh_wavemap_list wlist, const int order, cpl_table stab, const float ron2, const float gain)

static cpl_error_code	xsh_model_fill_obj (xsh_wavemap_list wlist, const int order, const double s1, const double s2, cpl_table stab, const float ron2, const float gain)

static cpl_error_code	xsh_model_fill_fit_bfit (xsh_wavemap_list wlist, const int order, cpl_table stab, const float ron2, const float gain)

static cpl_error_code	xsh_model_fill_fit_slice (xsh_wavemap_list wlist, const int order, const double s1, const double s2, cpl_table stab, const float ron2, const float gain)

static cpl_error_code	xsh_model_fill_fit_slice_bfit (xsh_wavemap_list wlist, const int order, const double s1, const double s2, cpl_table stab, const float ron2, const float gain)

static void	test_gsl_example (double data_x, double data_y, double data_e, double yfit, const int i_start, const size_t n, const size_t ncoeffs)

static void	xsh_gsl_bspline_non_uniform (double data_x, double data_y, double data_e, double bkpts, double *yfit, const int i_start, const size_t n, const size_t ncoeffs)

cpl_error_code	xsh_bspline_smooth_uniform_sl (cpl_table *tab, xsh_instrument instrument, const double s1, const double s2)

cpl_error_code	xsh_bspline_smooth_uniform (cpl_table *tab, xsh_instrument instrument)

static cpl_error_code	xsh_bspline_smooth_non_uniform2 (cpl_table bkpts, cpl_frame sky_orders_chunks, cpl_table *tab, const int iorder, xsh_instrument instrument)

static cpl_table *	xsh_fit_spline1 (xsh_wavemap_list wlist, int order, cpl_table sampl_tab, cpl_frame sky_orders_chunks, int sampl_pts_no, int iter_no, xsh_subtract_sky_single_param sky_par, float ron2, float gain, cpl_table **tab_line_res)
	This routine performs the B-SPLINE fit of a set of sky data non-uniformly sampled.

static cpl_table *	xsh_fit_spline2 (xsh_wavemap_list wlist, int order, cpl_table sampl_tab, cpl_frame sky_orders_chunks, int sampl_pts_no, int iter_no, xsh_subtract_sky_single_param sky_par, float ron2, float gain, cpl_table **tab_line_res)
	This routine performs the B-SPLINE fit of a set of sky data non-uniformly sampled.

static cpl_error_code	xsh_get_obj_and_sky_extraction_slits (xsh_subtract_sky_single_param sky_par, xsh_localization list, const double smap_min, const double smap_max, double obj_slit_min, double obj_slit_max, double sky_slit_min, double sky_slit_max)

static cpl_error_code	xsh_get_sky_edges_min_max_and_size (xsh_subtract_sky_single_param sky_par, const int miny, const int maxy, const int iorder, const int order, const int nx, const int wmap_xsize_diff, xsh_order_list ord_tab, cpl_image slitmap, double sky_slit_min, double sky_slit_max, int max_size, int *max_size_x)

static cpl_error_code	xsh_wavecal_list_pupulate (xsh_pre pre_sci, const int iorder, const int miny, const int maxy, const int wmap_xsize_diff, const int decode_bp, const double obj_slit_min, const double obj_slit_max, const double sky_slit_min, const double sky_slit_max, const int order, xsh_wavemap_list wave_list, int sky_size, xsh_order_list ord_tab, cpl_image wavemap, cpl_image slitmap)

static cpl_error_code	xsh_skycor_def_nbkpts_ord (const int iorder, const int nbkpts, cpl_frame break_pts_frame, xsh_instrument inst, int bspline_sampling_method, int *nbkpts_ord)

cpl_error_code	xsh_wavemap_list_full_sky_save (xsh_wavemap_list wave_list, xsh_instrument instr)

static void	xsh_obj_fit_dump (int iorder, xsh_wavemap_list *wave_list)

static cpl_error_code	xsh_subtract_sky_at_pix2 (const int all_size, const int sky_size, const int nx, wavemap_item pall, wavemap_item psky, float pflux, float pflat, float perrs, int pqual)

static cpl_error_code	xsh_subtract_sky_at_pix (const int sky_size, const int nx, wavemap_item psky, float pflux, float pflat, float perrs, int *pqual)

static cpl_error_code	xsh_subtract_sky_on_obj_at_pix (xsh_rec_list sky_list, const int iorder, const int object_size, const int nx, wavemap_item pobject, float pflux, float perrs, int pqual)

cpl_frame *	xsh_subtract_sky_single (cpl_frame sci_frame, cpl_frame order_table_frame, cpl_frame slitmap_frame, cpl_frame wavemap_frame, cpl_frame loc_table_frame, cpl_frame ref_sky_list, cpl_frame ref_sky_orders_chunks, cpl_frame usr_def_sampl_points, xsh_instrument instrument, int nbkpts, xsh_subtract_sky_single_param sky_par, cpl_frame sky_spectrum, cpl_frame sky_spectrum_eso, const char *rec_prefix, const int clean_tmp)
	Subtract the sky background for single frame. If sky_spectrum is NOT NULL it is saved as a product, of type REC.

cpl_frame *	xsh_save_sky_model (cpl_frame obj_frame, cpl_frame sub_sky_frame, const char sky_tag, xsh_instrument instrument)

cpl_frame *	xsh_add_sky_model (cpl_frame subsky_frame, cpl_frame sky_frame, xsh_instrument instrument, const char prefix)

Variables
double	xsh_nbkpts_uvb [XSH_ORDERS_UVB]
	Create the wavemap list.

double	xsh_nbkpts_vis [XSH_ORDERS_VIS]

double	xsh_nbkpts_nir [XSH_ORDERS_NIR]

Macros

Functions

Variables