xsh_utils.c File Reference

#include <assert.h>
#include <stdarg.h>
#include <time.h>
#include <math.h>
#include <stdlib.h>
#include <fcntl.h>
#include <sys/stat.h>
#include "xsh_utils.h"
#include <xsh_utils_wrappers.h>
#include <xsh_dfs.h>
#include <xsh_data_pre.h>
#include <xsh_dump.h>
#include <xsh_error.h>
#include <xsh_msg.h>
#include <xsh_parameters.h>
#include <xsh_data_spectrum.h>
#include <xsh_data_atmos_ext.h>
#include <xsh_pfits.h>
#include <xsh_pfits_qc.h>
#include <cpl.h>
#include <ctype.h>
#include <stdbool.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_multifit_nlin.h>
#include <gsl/gsl_version.h>

Go to the source code of this file.

Data Structures
struct	FRAME_DATE_IDX
struct	data

Macros
#define	MAXIMUM(x, y)   ((x) > (y)) ? (x) : (y)
#define	DEV_BLOCKSIZE   4096 /* used for fileutils_copy/move */
#define	XSH_ATM_EXT_UVB_WAV_MIN   310.
#define	CPL_TYPE   float
#define	CPL_TYPE_T   CPL_TYPE_FLOAT
#define	CPL_IMAGE_GET_DATA   cpl_image_get_data_float
#define	CPL_IMAGE_GET_DATA_CONST   cpl_image_get_data_float_const
#define	CPL_IMAGE_GET_MEDIAN   cpl_tools_get_median_float
#define	XSH_DOUBLE_SWAP(a, b)   { register double t=(a);(a)=(b);(b)=t; }
#define	XSH_FLOAT_SWAP(a, b)   { register float t=(a);(a)=(b);(b)=t; }
#define	XSH_INT_SWAP(a, b)   { register int t=(a);(a)=(b);(b)=t; }
#define	XSH_PIX_STACK_SIZE   50

Functions
void	xsh_random_init (void)
int	xsh_get_random_int_window (const int v1, const int v2)
	generates random integer values in range [v1,v2]
double	xsh_get_random_double_window (const double v1, const double v2)
	generates random integer values in range [v1,v2]
cpl_image *	xsh_imagelist_collapse_sigclip_iter_create (const cpl_imagelist *imlist, double sigma_low, double sigma_upp, const int niter)
	Average with sigma-clipping rejection an imagelist to a single image.
double	xsh_hms2deg (const double hms)
	Convert a double from hours minute seconds to deg:
double	xsh_sess2deg (const double sess)
	Convert a double from ssessagesimal to deg: 203049.197= 20:30:49.197 = 20.5136658333.
cpl_error_code	xsh_check_input_is_unbinned (cpl_frame *in)
	Check if an input frame is not binned.
int	xsh_fileutils_copy (const char *srcpath, const char *dstpath)
int	xsh_fileutils_move (const char *srcpath, const char *dstpath)
const char *	xsh_set_recipe_sky_file_prefix (char *rec_prefix)
	Set recipe sky frames prefix.
char *	xsh_set_recipe_file_prefix (cpl_frameset *raw, const char *recipe)
	Set recipe frames prefix.
cpl_error_code	xsh_set_cd_matrix (cpl_propertylist *plist)
	Set CD matrix.
cpl_error_code	xsh_set_cd_matrix1d (cpl_propertylist *plist)
	Set CD matrix.
cpl_error_code	xsh_set_cd_matrix2d (cpl_propertylist *plist)
	Set CD matrix.
cpl_error_code	xsh_set_cd_matrix3d (cpl_propertylist *plist)
	Set CD matrix.
cpl_parameterlist *	xsh_parameterlist_duplicate (const cpl_parameterlist *pin)
	Extract frames with given tag from frameset.
static void	xsh_property_dump (cpl_property *property)
	Dump property.
cpl_frame *	xsh_frameset_average (cpl_frameset *set, const char *tag)
	Dump propertylist.
cpl_frame *	xsh_frameset_add (cpl_frameset *set, xsh_instrument *instr, const int decode_bp)
	coadd frames in a frameset
void	xsh_plist_dump (cpl_propertylist *plist)
	Dump propertylist.
cpl_error_code	xsh_frameset_dump (cpl_frameset *set)
	Dump frameset.
cpl_error_code	xsh_frameset_dump_nod_info (cpl_frameset *set)
	Dump frameset nod info.
void	xsh_init (void)
	Reset library state.
char *	xsh_get_basename (const char *filename)
	Return base filename.
const char *	xsh_get_license (void)
	Get the pipeline copyright and license.
cpl_error_code	xsh_begin (cpl_frameset *frames, const cpl_parameterlist *parameters, xsh_instrument **instrument, cpl_frameset **raws, cpl_frameset **calib, const char *tag_list[], int tag_list_size, const char *recipe_id, unsigned int binary_version, const char *short_descr)
	Recipe initialization.
void	xsh_add_temporary_file (const char *name)
	Add temporary file to temprary files list.
void	xsh_free_temporary_files (void)
	Free temprary files list.
void	xsh_add_product_file (const char *name)
	Add temporary file to temprary files list.
void	xsh_free_product_files (void)
	Free temprary files list.
cpl_error_code	xsh_end (const char *recipe_id, cpl_frameset *frames, cpl_parameterlist *parameters)
	Recipe termination.
cpl_error_code	xsh_get_property_value (const cpl_propertylist *plist, const char *keyword, cpl_type keywordtype, void *result)
	Read a property value from a property list.
char *	xsh_stringdup (const char *s)
	String duplication.
char *	xsh_sdate_utc (time_t *now)
char *	xsh_stringcat (const char *s1, const char *s2)
	String concatenation.
char *	xsh_stringcat_3 (const char *s1, const char *s2, const char *s3)
	String concatenation.
char *	xsh_stringcat_4 (const char *s1, const char *s2, const char *s3, const char *s4)
	String concatenation.
char *	xsh_stringcat_5 (const char *s1, const char *s2, const char *s3, const char *s4, const char *s5)
	String concatenation.
char *	xsh_stringcat_6 (const char *s1, const char *s2, const char *s3, const char *s4, const char *s5, const char *s6)
	String concatenation.
char *	xsh_stringcat_any (const char *s,...)
	Concatenate an arbitrary number of strings.
int *	xsh_sort (void *base, size_t nmemb, size_t size, int(*compar)(const void *, const void *))
	Sort an array and give is index table.
void	xsh_reindex (double *data, int *idx, int size)
	TO BE DESCRIBED.
void	xsh_reindex_float (float *data, int *idx, int size)
	TO BE DESCRIBED.
void	xsh_reindex_int (int *data, int *idx, int size)
	TO BE DESCRIBED.
void	xsh_free (const void *mem)
	Deallocate memory.
void	xsh_free_image (cpl_image **i)
	Deallocate an image and set the pointer to NULL.
void	xsh_free_table (cpl_table **t)
	Deallocate a table and set the pointer to NULL.
void	xsh_free_mask (cpl_mask **m)
	Deallocate an image mask and set the pointer to NULL.
void	xsh_free_imagelist (cpl_imagelist **i)
	Deallocate an image list and set the pointer to NULL.
void	xsh_free_propertylist (cpl_propertylist **p)
	Deallocate a property list and set the pointer to NULL.
void	xsh_free_polynomial (cpl_polynomial **p)
	Deallocate a polynomial and set the pointer to NULL.
void	xsh_free_matrix (cpl_matrix **m)
	Deallocate a matrix and set the pointer to NULL.
void	xsh_free_parameterlist (cpl_parameterlist **p)
	Deallocate a parameter list and set the pointer to NULL.
void	xsh_free_parameter (cpl_parameter **p)
	Deallocate a parameter and set the pointer to NULL.
void	xsh_free_frameset (cpl_frameset **f)
	Deallocate a frame set and set the pointer to NULL.
void	xsh_free_frame (cpl_frame **f)
	Deallocate a frame and set the pointer to NULL.
void	xsh_free_vector (cpl_vector **v)
	Deallocate a vector and set the pointer to NULL.
void	xsh_free_array (cpl_array **m)
	Deallocate an array and set the pointer to NULL.
void	xsh_free_stats (cpl_stats **s)
	Deallocate a stats object and set the pointer to NULL.
void	xsh_unwrap_image (cpl_image **i)
	Unwrap an image and set the pointer to NULL.
void	xsh_unwrap_vector (cpl_vector **v)
	Unwrap a vector and set the pointer to NULL.
void	xsh_unwrap_array (cpl_array **a)
	Unwrap an array and set the pointer to NULL.
void	xsh_unwrap_bivector_vectors (cpl_bivector **b)
	Unwrap a bi-vector and set the pointer to NULL.
void	xsh_show_time (const char *comment)
	show time
void	xsh_tools_get_statistics (double *tab, int size, double *median, double *mean, double *stdev)
	Compute median, stdev and mean for the tab.
cpl_error_code	xsh_tools_sort_double (double *pix_arr, int n)
	Sort a double array.
cpl_error_code	xsh_tools_sort_float (float *pix_arr, int n)
	Sort a float array.
cpl_error_code	xsh_tools_sort_int (int *pix_arr, int n)
	Sort an integer array.
double	xsh_tools_get_median_double (double *array, int size)
	Calculates the median value of an array of double.
int	xsh_tools_running_median_1d_get_max (double *tab, int size, int wsize)
	get max of a list of doubles after running median
void	xsh_tools_min_max (int size, double *tab, double *min, double *max)
	computes min & max in ab array
cpl_vector *	xsh_tools_tchebitchev_poly_eval (int n, double X)
	Compute tchebitchev Tn(X) first coefficient for tchebitchev polynomial.
void	xsh_tools_tchebitchev_transform_tab (int size, double *pos, double min, double max, double *tcheb_pos)
	computes Tchebitchev transformation
double	xsh_tools_tchebitchev_transform (double pos, double min, double max)
	computes Tchebitchev transformation
double	xsh_tools_tchebitchev_reverse_transform (double pos, double min, double max)
	computes reverse Tchebitchev transformation
void	xsh_image_fit_spline (cpl_image *img, xsh_grid *grid)
	perform spline fit
void	xsh_vector_fit_gaussian (cpl_vector *x, cpl_vector *y, XSH_GAUSSIAN_FIT *result)
	set debug level
int	xsh_debug_level_set (int level)
	set debug level
int	xsh_debug_level_get (void)
	get debug level
const char *	xsh_debug_level_tostring (void)
	set debug level
int	xsh_time_stamp_set (int ts)
	set timestamp
int	xsh_time_stamp_get (void)
	get timestamp
void	xsh_mem_dump (const char *prompt)
double	convert_bin_to_data (double bin_data, int binning)
double	convert_data_to_bin (double data, int binning)
static double	date_to_double (const char *the_date)
static int	compare_frame_date (const void *one, const void *two)
cpl_frameset *	xsh_order_frameset_by_date (cpl_frameset *frameset)
	Order frameset by date.
polynomial *	xsh_polynomial_regression_2d (cpl_table *t, const char *X1, const char *X2, const char *Y, const char *sigmaY, int degree1, int degree2, const char *polynomial_fit, const char *residual_square, const char *variance_fit, double *mse, double *red_chisq, polynomial **variance, double kappa, double min_reject)
	Fit a 2d polynomial to three table columns.
int	xsh_select_table_rows (cpl_table *t, const char *column, cpl_table_select_operator operator, double value)
	Select table rows.
int	xsh_erase_table_rows (cpl_table *t, const char *column, cpl_table_select_operator operator, double value)
	Erase table rows.
cpl_frame *	xsh_frame_inv (cpl_frame *in, const char *filename, xsh_instrument *instr)
	Inverse the flux of a PRE frame.
cpl_frame *	xsh_frame_abs (cpl_frame *in, xsh_instrument *instr, cpl_frame **sign)
	Computes absolute value of a frame.
void	xsh_frame_spectrum_save (cpl_frame *frm, const char *name_o)
	save an spectrum frame
void	xsh_frame_image_save (cpl_frame *frm, const char *name_o)
	save an image frame
void	xsh_frame_table_save (cpl_frame *frame, const char *name_o)
	Save a table frame.
cpl_frame *	xsh_frame_mult (cpl_frame *in, xsh_instrument *instr, cpl_frame *sign)
	Computes product of two input frames.
cpl_error_code	xsh_monitor_flux (cpl_frame *frm_ima, const cpl_frame *frm_tab, xsh_instrument *instrument, const char *qc_key_prefix)
	Monitor Flux level along the orders traces given by an input table
cpl_error_code	xsh_update_pheader_in_image_multi (cpl_frame *frame, const cpl_propertylist *pheader)
	Update FITS header.
double	xsh_vector_get_err_median (cpl_vector *vect)
	Computes median error on a data set.
double	xsh_vector_get_err_mean (cpl_vector *vect)
	Computes mean error on a data set.
long	xsh_round_double (double x)
	Computes round(x)
int	xsh_min_int (int x, int y)
	Minimum of two numbers.
int	xsh_max_int (int x, int y)
	Maximum of two numbers.
double	xsh_min_double (double x, double y)
	Minimum of two numbers.
double	xsh_max_double (double x, double y)
	Maximum of two numbers.
double	xsh_pow_int (double x, int y)
	Computes x^y.
const char *	xsh_string_tolower (char *s)
	Convert all uppercase characters in a string into lowercase characters.
const char *	xsh_string_toupper (char *s)
	Convert all lowercase characters in a string into uppercase characters.
double	xsh_spline_hermite (double xp, const double *x, const double *y, int n, int *istart)
	Spline interpolation based on Hermite polynomials.
double	xsh_spline_hermite_table (double xp, const cpl_table *t, const char *column_x, const char *column_y, int *istart)
	Spline interpolation based on Hermite polynomials.
xsh_image_to_vector()
converts a fits image to a spectral vector Parameters spectrum 1-D Fits image that should be converted to a spectral vector Returns spectral vector with length lx*ly Note input image is destroyed
cpl_vector *	xsh_image_to_vector (cpl_image *spectrum)
cpl_image *	xsh_vector_to_image (const cpl_vector *vector, cpl_type type)
	Convert a vector to a 1d image.
cpl_frame *	xsh_util_multiply_by_response (cpl_frame *merged_sci, cpl_frame *response, const char *tag_o)
	Multiply input frame by response frame.
cpl_frame *	xsh_util_multiply_by_response_ord (cpl_frame *extracted_sci, cpl_frame *response, const char *tag_o)
	Multiply input frame by response frame.
static cpl_error_code	xsh_util_get_infsup (double *piw, double w, int i_start, int i_end, int *i_inf, int *i_sup)
static double	xsh_spectrum_integrate (double *pif, double *piw, int i1_inf, int i1_sup, int i2_inf, int i2_sup, double wave, double wstep)
cpl_frame *	xsh_spectrum_resample (cpl_frame *frame_inp, const double wstep, const double wmin, const double wmax, xsh_instrument *instr)
	resample a spectrum
cpl_frame *	xsh_util_frameset_collapse_mean (cpl_frameset *set, xsh_instrument *instrument)
	Compute mean frame from a list of (IMAGE) framesets.
cpl_error_code	xsh_normalize_spectrum_image_slice (const char *name_s, const char *tag_o, const int ext, const int bin_size, const double gain, const double exptime, const double airmass, const cpl_table *tbl_atm_ext)
	Normalize spectrum slice.
cpl_frame *	xsh_normalize_spectrum (const cpl_frame *obj_frame, const cpl_frame *atm_ext_frame, cpl_boolean correct_binning, xsh_instrument *instrument, const char *tag_o)
	Normalize a spectrum.
cpl_frame *	xsh_normalize_spectrum_ord (const cpl_frame *obj_frame, const cpl_frame *atm_ext_frame, cpl_boolean correct_binning, xsh_instrument *instrument, const char *tag_o)
	Normalize a spectrum.
cpl_image *	xsh_normalize_spectrum_image (const cpl_image *spectrum, const cpl_image *spectrum_error, const cpl_propertylist *spectrum_header, const int bin_size, const double gain, const double exptime, const double airmass, const int n_traces, const cpl_table *atm_extinction, cpl_image **scaled_error)
	Normalize a spectrum.
static double	xsh_iterpol_linear (double *data_x, double *data_y, int ndata, double x, int *i_inf, int *i_sup)
cpl_frame *	xsh_spectrum_interpolate_linear (cpl_frame *table_frame, const double wstep, const double wmin, const double wmax)
	spectra interpolation
cpl_frame *	xsh_spectrum_interpolate (cpl_frame *table_frame, const double wstep, const double wmin, const double wmax)
	spectra interpolation
void	xsh_array_clip_mean (cpl_array *array, double kappa, int niter, double frac_min, double *mean, double *stdev)
	mean clip of an array
void	xsh_array_clip_median (cpl_array *array, double kappa, int niter, double frac_min, double *median, double *stdev)
	median clip of an array
void	xsh_array_clip_poly1d (cpl_vector *pos_vect, cpl_vector *val_vect, double kappa, int niter, double frac_min, int deg, cpl_polynomial **polyp, double *chisq, int **flagsp)
	clip outliers from a 1D poly fit
cpl_error_code	xsh_rectify_params_set_defaults (cpl_parameterlist *pars, const char *rec_id, xsh_instrument *inst, xsh_rectify_param *rectify_par)
cpl_error_code	xsh_remove_crh_single_params_set_defaults (cpl_parameterlist *pars, const char *rec_id, xsh_instrument *inst, xsh_remove_crh_single_param *crh_single_par)
static int	expb_f (const gsl_vector *x, void *data, gsl_vector *f)
static int	expb_df (const gsl_vector *x, void *data, gsl_matrix *J)
static int	expb_fdf (const gsl_vector *x, void *data, gsl_vector *f, gsl_matrix *J)
void	xsh_gsl_init_gaussian_fit (cpl_vector *xpos_vect, cpl_vector *ypos_vect, double *init_par)
void	xsh_gsl_fit_gaussian (cpl_vector *xpos_vect, cpl_vector *ypos_vect, int deg, double *params, double *errs, int *status)
xsh_xcorrelate
@memo Cross-correlation of two 1d signals. Parameters line_i The reference signal. width_i Number of samples in reference signal. line_t Candidate signal to compare. width_t Number of samples in candidate signal. half_search Half-size of the search domain. delta Output sinfo_correlation offset. Returns Maximum cross-correlation value as a double. @doc Two signals are expected in input of this function: a reference signal (line_i) and a candidate signal (line_t) . They are expected to be roughly the same signal up to an offset (delta) A cross-correlation is computed on 2*half_search+1 values. The maximum of likelihood is the maximum cross-correlation value between signals. The offset 'delta' corresponding to this position is returned. Returns -100.0 in case of error. Normally, the cross-sinfo_correlation coefficient is normalized so it should stay between -1 and +1.
double *	xsh_function1d_xcorrelate (double *line_i, int width_i, double *line_t, int width_t, int half_search, int normalise, double *xcorr_max, double *delta)
int	raw_mjd_frame_compare (const cpl_frame *f1, const cpl_frame *f2)
cpl_error_code	get_average_qc_from_raws (cpl_frameset *fset, xsh_instrument *instrument, cpl_propertylist *qclist)
cpl_error_code	get_chromatic_eff (cpl_frame *eff, cpl_propertylist *qclist)
cpl_error_code	calc_curve_qc (cpl_image *im, xsh_instrument *instrument, cpl_propertylist *qclist)
static int	qc_linfunc (const double x[], const double p[], double *f)
static int	qc_dlinfunc (const double x[], const double p[], double f[])
cpl_error_code	calc_flat_slit_qc (cpl_image *im, int xa1, int xa2, cpl_propertylist *qclist)
cpl_error_code	calc_resp_qc (cpl_table *mtab, cpl_table *rtab, xsh_instrument *instrument, int lower, int upper, const char *label, cpl_propertylist *qclist)

Variables
static int	XshDebugLevel = XSH_DEBUG_LEVEL_NONE
static int	XshTimeStamp = FALSE
static char **	TempFiles = NULL
static int	NbTemp = 0
static char **	ProdFiles = NULL
static int	NbProducts = 0

Macro Definition Documentation

DEV_BLOCKSIZE

#define DEV_BLOCKSIZE   4096 /* used for fileutils_copy/move */

Definition at line 78 of file xsh_utils.c.

MAXIMUM

#define MAXIMUM	(		x,
			y
	)		((x) > (y)) ? (x) : (y)

Definition at line 75 of file xsh_utils.c.

XSH_ATM_EXT_UVB_WAV_MIN

#define XSH_ATM_EXT_UVB_WAV_MIN   310.

Definition at line 79 of file xsh_utils.c.

Variable Documentation

XshDebugLevel

int XshDebugLevel = XSH_DEBUG_LEVEL_NONE

static

Definition at line 69 of file xsh_utils.c.

Referenced by xsh_debug_level_get(), xsh_debug_level_set(), and xsh_debug_level_tostring().

XshTimeStamp

int XshTimeStamp = FALSE

static

Definition at line 70 of file xsh_utils.c.

Referenced by xsh_time_stamp_get(), and xsh_time_stamp_set().