/**
* Function: get_fits_header
* Returns the header of extension hdunum from a fits file filename
*
* Parameters:
* @param filename The name of the FITS file
* @param hdunum the number of the HDU to access
*
* Returns:
* @return a pointer to a newly allocated string containing the entire header
*/
char *
get_fits_header (char filename[], int hdunum)
{
fitsfile *input;
int f_status = 0, hdutype;
int nkeys, i;
char card[FLEN_CARD];
char *header, *p;
// Open the file for creating/appending
fits_open_file (&input, filename, READONLY, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_fits_header: Could not open" " file:", filename);
}
fits_movabs_hdu (input, hdunum, &hdutype, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_fits_header: "
"Could not read extention %d from file: %s", hdunum,
filename);
}
fits_get_hdrspace (input, &nkeys, NULL, &f_status); /* get # of keywords */
header = (char *) malloc ((nkeys + 1) * FLEN_CARD * sizeof (char));
p = header;
for (i = 0; i < nkeys; i++)
{ /* Read and print each keywords */
if (fits_read_record (input, i + 1, card, &f_status))
break;
sprintf(p,"%-80s", card);
p = p + 80;
}
/* Add END keyword */
sprintf (card, "END");
sprintf(p,"%-80s", card);
return header;
}
/**
* Function: get_lcolumn_from_SPC_opened
* The function reads the values from a column with long specified
* by its name into a array of type long. The array is returned.
*
* Parameters:
* @param SPC_ptr - pointer to the SPC extension
* @param count_col - name of the column to load
* @param nelems - number of elements in the column
*
* Returns:
* @return values - pointer to a filled array
*/
long *
get_lcolumn_from_SPC_opened(fitsfile *SPC_ptr, char colname[], int nelems)
{
int colnum=0;
int anynul;
int f_status=0;
long *values;
// allocate the return array;
// give an error if allocation fails
values = (long *) malloc(nelems * sizeof(long));
if (!values) {
aXe_message (aXe_M_ERROR, __FILE__, __LINE__,
"Memory allocation failed");
}
// get the desired column number;
// give an error if the column name
// can not be read
fits_get_colnum (SPC_ptr, CASEINSEN, colname, &colnum, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_dcolumn_from_SPC_opened: "
"Could not determine column %s in "
" table!\n", colname);
}
// read all data in the column
fits_read_col (SPC_ptr, TLONG, colnum, 1, 1, nelems, NULL, values,
&anynul, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_dcolumn_from_SPC_opened: "
"Could not read column %s"
" from BINARY table!",colname);
}
// return the filled array
return values;
}
/**
* Function: get_SPC_opened
* The function opens an existing SPC file and returns the pointer
* to it.
* As of now, the mode of opening it is automatically READWRITE.
* Later on a differentiation using the free parameter "mode"
* might be added to generalize the function.
*
* Parameters:
* @param SPCname - name of the SPC file
* @param mode - mode to open it (not yet used)
*
* Returns:
* @return SPC_ptr - pointer to the opened fits file
*
*/
fitsfile *
get_SPC_opened(char SPCname[], int mode)
{
fitsfile *SPC_ptr;
int f_status=0;
// Open the OPET file for reading/writing
fits_open_file (&SPC_ptr, SPCname, READWRITE, &f_status);
if (f_status)
{
ffrprt (stdout, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_INTPIXCORR: Could not open file: %s\n",
SPCname);
}
// return the pointer to the fits file
return SPC_ptr;
}
/**
* Function: get_num_extensions
* The function determines the number of extensions in
* the fits file. Here the primary extension does not count.
*
* Parameters:
* @param spectral_models_file - pathname to the spectral models file
*
* Returns:
* @return n_models - the number of spectral models
*/
int
get_num_extensions(const char spectral_models_file[])
{
int n_ext=0;
int n_models=0;
int i;
int f_status=0;
fitsfile *s_models;
// open the fits file
// report any error
fits_open_file (&s_models, spectral_models_file, READONLY, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PETCONT: " "Could not open file: %s",
spectral_models_file);
}
// do until a fits error occurs
while (!f_status)
{
// move one extension forward
fits_movrel_hdu (s_models, 1, NULL, &f_status);
// count up
n_ext++;
}
// close the fits file
fits_close_file (s_models, &f_status);
// the zeroth extension
// does nnot count!!
n_models = n_ext - 1;
// return the
return n_models;
}
int
main (int argc, char *argv[])
{
char *opt;
char grism_file[MAXCHAR];
char grism_file_path[MAXCHAR];
char aper_file[MAXCHAR];
char aper_file_path[MAXCHAR];
char obj_PET_file[MAXCHAR];
char obj_PET_file_path[MAXCHAR];
char bck_PET_file[MAXCHAR];
char bck_PET_file_path[MAXCHAR];
char conf_file[MAXCHAR];
char conf_file_path[MAXCHAR];
char SPC_file[MAXCHAR];
char SPC_file_path[MAXCHAR];
char SPC_opt_file[MAXCHAR];
char SPC_opt_file_path[MAXCHAR];
char WHT_file[MAXCHAR];
char WHT_file_path[MAXCHAR];
char label[MAXCHAR];
int i, index, dobck = 0, noflux = 1;
object **oblist;
FITScards *cards;
ap_pixel *obj_PET = NULL, *bck_PET = NULL;
observation *obs;
//tracestruct *trace;
aperture_conf *conf;
spectrum *obj_spec = NULL, *bck_spec = NULL, *sobj_spec = NULL;
spectrum *resp;
response_function *resp_func;
calib_function *wl_calibration;
fitsfile *OPET_ptr, *BPET_ptr;
int f_status = 0;
fitsfile *SPC_ptr, *SPC_opt_ptr, *WHT_ptr;
gsl_matrix *weights;
drzstamp *modvar;
int obj_aperID, obj_beamID, objindex;
int bck_aperID, bck_beamID;
char table[MAXCHAR], table_path[MAXCHAR];
//char comment[FLEN_COMMENT];
int empty;
int drizzle;
int quant_cont=0;
int opt_weights=0;
int for_grism=0;
int smooth_conv=0;
d_point smooth_params;
double exptime;
double sky_cps;
drzstamp_dim dimension;
gsl_matrix *coverage;
if (((argc < 3))
|| (opt = get_online_option ("help", argc, argv)))
{
fprintf (stdout,
"ST-ECF European Coordinating Facility\n"
"Copyright (C) 2002 Martin Kuemmel\n"
"aXe_PET2SPC Version %s:\n"
" aXe task that produces 1-D, binned spectra using information\n"
" contained in a OPET and a BPET. A 1-D spectrum is generated\n"
" for each beam in each of both the OPET and the BPET files\n"
" The binned background spectra of each beam (order) is then\n"
" subtraced from the corresponding spectra form the OPET. Th\ne"
" background subtraction (and reading a BPET altogether can be\n"
" avoided by using the -noBPET option\n"
" An SPC file, a multi-extension FITS file containing binned\n"
" spectra is produced. Each extension (named after the beam ID,\n"
" e.g. 11B for aperture (object) 11,beam (order) B) contains the\n"
" following columns:\n"
"\n"
" LAMBDA ; the wavelength (in A)\n"
" TCOUNT ; the total number of counts (in DN)\n"
" TERROR ; the error in TERRORS (in DN)\n"
" BCOUNT ; the estimated number of counts from the\n"
" background (in DN)\n"
" BERROR ; the error in BCOUNTS (in DN)\n"
" COUNT ; the estimated number of counts from the\n"
" object (in DN)\n"
" ERROR ; the error in COUNTS (in DN)\n"
" FLUX ; the estimated flux (in erg/s/cm^2/A)\n"
" FERROR ; the error in FLUX (in erg/s/cm^s/A)\n"
" WEIGHT ; weight (in pixels)\n"
"\n"
" Input FITS mages are looked for in $AXE_IMAGE_PATH\n"
" aXe config file is looked for in $AXE_CONFIG_PATH\n"
" All outputs are writen to $AXE_OUTPUT_PATH\n"
"\n"
"Usage:\n"
" aXe_PET2SPC [g/prism image filename] [aXe config file name] [options]\n"
"\n"
"Options:\n"
" -noBPET - to disable the use of a BPET file\n"
" -noflux - to disable the flux calibration\n"
" -drz - use $AXE_DRIZZLE_PATH to locate the grism-, OAF-\n"
" - and PET-files instead of $AXE_IMAGE/OUTPUT_PATH\n"
" -in_AF=[string] - overwrite the default input Aperture File name\n"
" -OPET=[string] - overwrite the default input Object PET file name\n"
" -BPET=[string] - overwrite the default input Background PET\n"
" file name\n"
" -out_SPC=[string] - overwrite the default output SPC file name\n"
"\n"
"Example:\n"
" ./aXe_PET2SPC slim_grism.fits SLIM.conf.A.0\n"
"\n",RELEASE);
exit (1);
}
// make a general opening statement
fprintf (stdout, "aXe_PET2SPC: Starting...\n");
// get the name of the flt-file
index = 0;
strcpy (grism_file, argv[++index]);
if ((opt = get_online_option ("drz", argc, argv)))
{
build_path (AXE_DRIZZLE_PATH, grism_file, grism_file_path);
drizzle=1;
}
else
{
build_path (AXE_IMAGE_PATH, grism_file, grism_file_path);
drizzle=0;
}
// get the name of the configuration file
strcpy (conf_file, argv[++index]);
build_path (AXE_CONFIG_PATH, conf_file, conf_file_path);
// load the configuration file
conf = get_aperture_descriptor (conf_file_path);
// Determine where the various extensions are in the FITS file
get_extension_numbers(grism_file_path, conf,conf->optkey1,conf->optval1);
// Build aperture file name
replace_file_extension (grism_file, aper_file, ".fits",
".OAF", conf->science_numext);
if (drizzle)
build_path (AXE_DRIZZLE_PATH, aper_file, aper_file_path);
else
build_path (AXE_OUTPUT_PATH, aper_file, aper_file_path);
// Build object PET file name
replace_file_extension (grism_file, obj_PET_file, ".fits",
".PET.fits", conf->science_numext);
// make the total filename
if (drizzle)
build_path (AXE_DRIZZLE_PATH, obj_PET_file, obj_PET_file_path);
else
build_path (AXE_OUTPUT_PATH, obj_PET_file, obj_PET_file_path);
// Build background PET file name
replace_file_extension (grism_file, bck_PET_file, ".fits",
".BCK.PET.fits", conf->science_numext);
// make the total filename
if (drizzle)
build_path (AXE_DRIZZLE_PATH, bck_PET_file, bck_PET_file_path);
else
build_path (AXE_OUTPUT_PATH, bck_PET_file, bck_PET_file_path);
// make a non-standard AF name if necessary
if ((opt = get_online_option ("in_AF", argc, argv)))
{
strcpy(aper_file,opt);
strcpy(aper_file_path,opt);
}
// make a non-standard PET name if necessary
if ((opt = get_online_option ("OPET", argc, argv)))
{
strcpy(obj_PET_file,opt);
strcpy(obj_PET_file_path,opt);
}
// make a non-standard BPET name if necessary
if ((opt = get_online_option ("BPET", argc, argv)))
{
strcpy(bck_PET_file,opt);
strcpy(bck_PET_file_path,opt);
}
// set the flagg for no background subtraction
if ((opt = get_online_option ("noBPET",argc,argv)))
{
dobck = 0;
strcpy(bck_PET_file,"None");
strcpy(bck_PET_file_path, "None");
}
else
{
dobck = 1;
}
// set the flagg for flux
if ((opt = get_online_option ("noflux",argc,argv)))
noflux = 1;
else
noflux = 0;
// check for the weights flagg,
// set the file name if the flagg is set
if ((opt = get_online_option ("opt_weights",argc,argv)))
opt_weights = 1;
else
opt_weights = 0;
// read the trigger for smoothing the sensitivity
if ((opt = get_online_option ("smooth_conv",argc,argv)))
smooth_conv = 1;
else
smooth_conv = 0;
if ((opt = get_online_option ("out_SPC", argc, argv)))
{
strcpy (SPC_file, opt);
strcpy (SPC_file_path, opt);
if (opt_weights)
{
replace_file_extension (SPC_file, SPC_opt_file, ".fits",
"_opt.SPC.fits", -1);
replace_file_extension (SPC_file_path, SPC_opt_file_path, ".fits",
"_opt.SPC.fits", -1);
replace_file_extension (SPC_opt_file, WHT_file, ".SPC.fits",
".WHT.fits", -1);
replace_file_extension (SPC_opt_file_path, WHT_file_path, ".SPC.fits",
".WHT.fits", -1);
}
}
else
{
replace_file_extension (obj_PET_file, SPC_file, ".PET.fits",
".SPC.fits", -1);
if (drizzle)
build_path (AXE_DRIZZLE_PATH, SPC_file, SPC_file_path);
else
build_path (AXE_OUTPUT_PATH, SPC_file, SPC_file_path);
if (opt_weights)
{
replace_file_extension (obj_PET_file, SPC_opt_file, ".PET.fits",
"_opt.SPC.fits", -1);
replace_file_extension (SPC_opt_file, WHT_file, ".SPC.fits",
".WHT.fits", -1);
if (drizzle)
{
build_path (AXE_DRIZZLE_PATH, SPC_opt_file, SPC_opt_file_path);
build_path (AXE_DRIZZLE_PATH, WHT_file, WHT_file_path);
}
else
{
build_path (AXE_OUTPUT_PATH, SPC_opt_file, SPC_opt_file_path);
build_path (AXE_OUTPUT_PATH, WHT_file, WHT_file_path);
}
}
}
// check the configuration file for the smoothin keywords
if (!check_conf_for_smoothing(conf, smooth_conv))
aXe_message(aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SP: Either the configuration file %s does not contain\n"
"the necessary keywords for the smoothing (POBJSIZE, SMFACTOR),\n"
"or one of these keywords has an unreasonable value < 0.0!\n",
conf_file_path);
// give feedback onto the screen:
// report on input and output
// and also on specific parameter
fprintf (stdout, "aXe_PET2SPC: Input configuration file name: %s\n",
conf_file_path);
fprintf (stdout, "aXe_PET2SPC: Input Object Aperture file name: %s\n",
aper_file_path);
fprintf (stdout, "aXe_PET2SPC: Input Object PET file name: %s\n",
obj_PET_file_path);
if (dobck)
fprintf (stdout, "aXe_PET2SPC: Input Background PET file name: %s\n",
bck_PET_file_path);
fprintf (stdout, "aXe_PET2SPC: Output SPC file name: %s\n",
SPC_file_path);
if (opt_weights)
{
fprintf (stdout, "aXe_PET2SPC: Computing optimal weights.\n");
fprintf (stdout, "aXe_PET2SPC: Optimized SPC file name: %s\n",
SPC_opt_file_path);
fprintf (stdout, "aXe_PET2SPC: Output WHT file name: %s\n",
WHT_file_path);
}
if (!noflux)
{
fprintf (stdout, "aXe_PET2SPC: Performing flux calibration.\n");
if (smooth_conv)
fprintf (stdout, "aXe_PET2SPC: Using smoothed sensitivity curves.\n");
}
fprintf (stdout, "\n\n");
//
// try to get the descriptor 'exptime' from the 'sci'-extension
//
exptime = (double)get_float_from_keyword(grism_file_path, conf->science_numext, conf->exptimekey);
if (isnan(exptime))
exptime = (double)get_float_from_keyword(grism_file_path, 1, conf->exptimekey);
if (isnan(exptime))
exptime = 1.0;
//
// try to get the descriptor 'SKY_CPS' from the 'sci'-extension
//
sky_cps = (double)get_float_from_keyword(grism_file_path, conf->science_numext, "SKY_CPS");
if (isnan(sky_cps))
sky_cps = 0.0;
// Open the OPET file for reading
fits_open_file (&OPET_ptr, obj_PET_file_path, READONLY, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SPC: Could not open file: %s\n",
obj_PET_file_path);
}
// check whether the contamination is quantitative
quant_cont = check_quantitative_contamination(OPET_ptr);
if (opt_weights && !quant_cont)
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SPC: The optimal extractions needs quantitative contamination! "
" Please re-run aXe with Gauss or Fluxcube contamination!");
obs = load_dummy_observation ();
/* Loading the object list */
fprintf (stdout, "aXe_PET2SPC: Loading object aperture list...");
oblist = file_to_object_list_seq (aper_file_path, obs);
fprintf (stdout,"%d objects loaded.\n",object_list_size(oblist));
if (dobck)
{
// Open the file for reading
fits_open_file (&BPET_ptr, bck_PET_file_path, READONLY, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SP: Could not open file: %s\n",
bck_PET_file_path);
}
}
/* Copy the header info from the grism image */
SPC_ptr = create_SPC_opened (SPC_file_path,1);
cards = get_FITS_cards_opened(OPET_ptr);
put_FITS_cards_opened(SPC_ptr, cards);
free_FITScards(cards);
if (opt_weights)
{
cards = get_FITS_cards_opened(OPET_ptr);
// open the WHT file and add the header keywords
WHT_ptr = create_FITSimage_opened (WHT_file_path, 1);
put_FITS_cards_opened(WHT_ptr, cards);
// open the opt_SPC and add the header keywords
SPC_opt_ptr = create_SPC_opened (SPC_opt_file_path,1);
put_FITS_cards_opened(SPC_opt_ptr, cards);
// delete the header keywords
free_FITScards(cards);
}
// do something only if there
// exist valid objects
i = 0;
if (oblist!=NULL)
{
// turn until the end of the PET is reached
while (1)
{
empty=0;
// Get the PET for this object
obj_PET = get_ALL_from_next_in_PET(OPET_ptr, &obj_aperID, &obj_beamID);
// load the background PET if requested
if (dobck)
{
bck_PET = get_ALL_from_next_in_PET(BPET_ptr, &bck_aperID, &bck_beamID);
if ((bck_aperID!=obj_aperID)||(bck_beamID!=obj_beamID))
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"Background PET and Object PET extensions are not"
" in the same order and cannot be combined.\n");
}
// end of PET reached: the break condition
if ((obj_aperID==-1) && (obj_beamID==-1))
break;
// signal an empty PET
if (obj_PET==NULL)
empty=1;
// give feedback to the screen
fprintf (stdout, "aXe_PET2SPC: BEAM %d; %d%c\n", i, obj_aperID, BEAM(obj_beamID));fflush(stdout);
// identify the object which matches the PET
objindex = find_object_in_object_list(oblist,obj_aperID);
// look whether we are for grisms or prisms
for_grism = check_for_grism (conf_file_path, obj_beamID);
wl_calibration = get_calfunc_for_beam(oblist[objindex]->beams[obj_beamID], for_grism, conf_file_path, conf);
// compute the object spectrum
obj_spec = bin_naive (obj_PET, oblist[objindex]->beams[obj_beamID].width,
oblist[objindex]->beams[obj_beamID].orient, quant_cont);
// check for the existence of a background PET
if (dobck)
{
// compute the background spectrum
bck_spec = bin_naive (bck_PET,
oblist[objindex]->beams[bck_beamID].width,
oblist[objindex]->beams[bck_beamID].orient, quant_cont);
}
else
{
// create a dummy background spectrum
bck_spec = empty_counts_spectrum_copy(obj_spec);
}
// subtract the background spectrum from the
// object (or forground) spectrum
sobj_spec = subtract_spectra (obj_spec, bck_spec);
if(!noflux)
{
get_troughput_table_name(conf_file_path,
oblist[objindex]->beams[obj_beamID].ID,
table);
if (strcmp(table,"None"))
{
build_path (AXE_CONFIG_PATH, table, table_path);
resp=get_response_function_from_FITS(table_path,2);
resp_func = create_response_function(table_path);
if (resp->spec_len <2)
{
aXe_message (aXe_M_WARN1, __FILE__, __LINE__,
"Throughput table %s contains only %d"
" values. No sensitivity curve was applied.\n",
table_path,resp->spec_len);
}
else
{
fprintf(stdout,"aXe_PET2SPC: Applying sensitivity contained in %s\n",table_path);
smooth_params = get_smooth_pars_for_beam(conf, smooth_conv, oblist[objindex]->beams[obj_beamID]);
if (smooth_params.x > 0.0)
{
// apply a smoothed flux conversion
apply_smoothed_response(wl_calibration, for_grism, quant_cont, resp_func, smooth_params, sobj_spec);
}
else
{
// apply a normal flux conversion
apply_response_function(sobj_spec,resp, quant_cont);
}
}
// free the memory of the
// response functions
free_spectrum(resp);
free_response_function(resp_func);
}
}
if (empty!=1)
{
add_spectra_to_SPC_opened (SPC_ptr, obj_spec, bck_spec,
sobj_spec, oblist[objindex]->ID, oblist[objindex]->beams[obj_beamID].ID);
/* Copy header from OPET extension into this SPC extension */
cards = get_FITS_cards_opened(OPET_ptr);
put_FITS_cards_opened(SPC_ptr,cards);
free_FITScards(cards);
}
free_spectrum (bck_spec);
free_spectrum (sobj_spec);
free_spectrum (obj_spec);
if (opt_weights)
{
// get the dimension in trace length
// and crossdispersion
dimension = get_all_dims(obj_PET, bck_PET,
oblist[objindex]->beams[obj_beamID], dobck);
// check for empty PET
if (!dimension.resolution)
{
// create dummies in case of empty PET's
weights = get_default_weight();
modvar = get_default_modvar();
}
else
{
// prepare the PET's by computing the inverse variance.
// Also the trace distances are shifted by 0.5
// to get a sampling comparable to the unweighted
// extraction
prepare_inv_variance(obj_PET, bck_PET, dobck, conf, exptime, sky_cps, 0.0);
// compute the inverse variance and the profile
// image in the trace distance - crossdispersion plane
modvar = compute_modvar(obj_PET, oblist[objindex]->beams[obj_beamID], dimension);
// compute the optimal weights
weights = comp_allweight(modvar);
}
if (dimension.resolution && empty != 1)
{
sprintf (label, "WHT_%d%c", obj_aperID, BEAM (obj_beamID));
gsl_to_FITSimage_opened (weights, WHT_ptr ,0,label);
// make and store the default header
cards = beam_to_FITScards(oblist[objindex],obj_beamID);
put_FITS_cards_opened(WHT_ptr,cards);
free_FITScards(cards);
}
// create the optimal weighted
// foreground spectrum
obj_spec = bin_optimal (obj_PET,oblist[objindex]->beams[obj_beamID],
quant_cont, weights, dimension, coverage);
// check for the presence of a background PET
if (dobck)
{
// create the optimal weighted
// background spectrum
bck_spec = bin_optimal (bck_PET,oblist[objindex]->beams[obj_beamID],
quant_cont, weights, dimension, coverage);
}
else
{
// make a dummy background spectrum
bck_spec = empty_counts_spectrum_copy(obj_spec);
}
// release memory
gsl_matrix_free(weights);
free_drzstamp(modvar);
// subtract the background spectrum from the
// object (or forground) spectrum
sobj_spec = subtract_spectra (obj_spec, bck_spec);
if(!noflux)
{
get_troughput_table_name(conf_file_path,
oblist[objindex]->beams[obj_beamID].ID,
table);
if (strcmp(table,"None"))
{
build_path (AXE_CONFIG_PATH, table, table_path);
resp=get_response_function_from_FITS(table_path,2);
resp_func = create_response_function(table_path);
if (resp->spec_len <2)
{
aXe_message (aXe_M_WARN1, __FILE__, __LINE__,
"Throughput table %s contains only %d"
" values. No sensitivity curve was applied.\n",
table_path,resp->spec_len);
}
else
{
fprintf(stdout,"aXe_PET2SPC: Applying sensitivity contained in %s\n",table_path);
smooth_params = get_smooth_pars_for_beam(conf, smooth_conv, oblist[objindex]->beams[obj_beamID]);
if (smooth_params.x > 0.0)
{
apply_smoothed_response(wl_calibration, for_grism, quant_cont, resp_func, smooth_params, sobj_spec);
}
else
{
apply_response_function(sobj_spec,resp, quant_cont);
}
}
// free the memory
free_spectrum(resp);
free_response_function(resp_func);
}
}
if (empty!=1)
{
add_spectra_to_SPC_opened (SPC_opt_ptr, obj_spec, bck_spec,
sobj_spec, oblist[objindex]->ID, oblist[objindex]->beams[obj_beamID].ID);
/* Copy header from OPET extension into this SPC extension */
cards = get_FITS_cards_opened(OPET_ptr);
put_FITS_cards_opened(SPC_opt_ptr,cards);
free_FITScards(cards);
}
free_spectrum (bck_spec);
free_spectrum (sobj_spec);
free_spectrum (obj_spec);
}
// free memory
free_calib (wl_calibration);
if (bck_PET!=NULL)
free (bck_PET);
if (obj_PET!=NULL)
free (obj_PET);
i++;
}
}
fits_close_file (SPC_ptr, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SPC: " "Error closing SPC: %s\n",
SPC_file_path);
}
if (opt_weights)
{
fits_close_file (WHT_ptr, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SPC: " "Error closing WHT: %s\n",
WHT_file_path);
}
fits_close_file (SPC_opt_ptr, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_PET2SPC: " "Error closing PSC: %s\n",
SPC_opt_file_path);
}
}
if (oblist!=NULL)
free_oblist (oblist);
fprintf (stdout, "aXe_PET2SPC: Done...\n");
exit (0);
}
/**
* Function: get_ALL_from_next_in_SPC
* The function creates and fills a full spectrum structure with
* the content of a SPC table extension. This is only done when,
* according to the beam ID, this beam should be corrected.
* For extensions with higher order beams which are not corrected
* an emply structure is returned.
*
* Parameters:
* @param SPCn_ptr - pointer to the opened SPC file
* @param aperID - pointer to aperture identification number
* @param beamID - pointer to beam identification number
*
* Returns:
* @return SPC - the full spectrum structure
*/
full_spectr *
get_ALL_from_next_in_SPC(fitsfile *SPC_ptr, int *aperID, int *beamID)
{
int f_status=0, hdutype;
long tmp;
//long nrows=0;
char comment[FLEN_COMMENT];
full_spectr *SPC;
fits_movrel_hdu (SPC_ptr, 1, &hdutype, &f_status);
if (f_status)
{
*aperID = -1;
*beamID = -1;
SPC = NULL;
return SPC;
}
// read the beam ID number
fits_read_key_lng (SPC_ptr, "BEAMID", &tmp, comment, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_ALL_from_next_in_SPC: Error getting index keyword OBJECTID");
}
*beamID = (int)tmp;
// check whether this beam should be correct
if (*beamID > CORRMAX)
{
// set it to NULL and return
SPC = NULL;
// fprintf (stdout, "aXe_PETFF: Skipping beam: %c.\n", BEAM(*beamID));
return SPC;
}
// the beam shall be corrected and
// first must be read in
SPC = (full_spectr *) malloc (sizeof (full_spectr ));
// transfer the beam ID
SPC->beamID = (int)tmp;
// read the aperture number
fits_read_key_lng (SPC_ptr, "OBJECTID", &tmp, comment, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_ALL_from_next_in_SPC: Error getting index keyword OBJECTID");
}
// transfer the aperture ID
*aperID = (int)tmp;
SPC->aperID = (int)tmp;
// Get the number of rows
fits_get_num_rows (SPC_ptr, &tmp, &f_status);
if (f_status) {
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"get_ALL_from_next_in_SPC: "
"Could not determine the number of rows in"
" correction function table!");
}
SPC->nelems = (int)tmp;
// load the background subtracted object spectrum
SPC->obj_spec = get_spectrum_from_SPC(SPC_ptr, "COUNT", "ERROR", SPC->nelems);
// load the total object spectrum
SPC->fgr_spec = get_spectrum_from_SPC(SPC_ptr, "TCOUNT", "TERROR", SPC->nelems);
// load the background spectrum
SPC->bck_spec = get_spectrum_from_SPC(SPC_ptr, "BCOUNT", "BERROR", SPC->nelems);
// return the filled structure
return SPC;
}
/**
* Function: load_SED_from_fitsext
* The function creates a energy distribution from the data stored
* in a fits file extension. The data must be stored in the columns
* "wavelength" and "flux".
*
* Parameters:
* @param spectral_models_file - pathname to the spectral models file
* @param s_models - pointer to the fits file extension
*
* Returns:
* @return sed - the energy distribution created
*/
energy_distrib *
load_SED_from_fitsext(const char spectral_models_file[], fitsfile *s_models)
{
int f_status=0;
int anynul;
long nrows=0;
int colnum1;
int colnum2;
energy_distrib *sed;
double *sed_wavs;
double *sed_flux;
// allocate memory for the energy distribution
sed = (energy_distrib *) malloc(sizeof(energy_distrib));
// get number of rows
fits_get_num_rows (s_models, &nrows, &f_status);
if (f_status) {
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"load_SED_from_fitsext: "
"Could not determine the number of rows in"
" table %s",spectral_models_file);
}
// allocate memory for the data
sed_wavs = (double *) malloc(nrows*sizeof(double));
if (!sed_wavs) {
aXe_message (aXe_M_ERROR, __FILE__, __LINE__,
"Memory allocation failed");
}
sed_flux = (double *) malloc(nrows*sizeof(double));
if (!sed_flux) {
aXe_message (aXe_M_ERROR, __FILE__, __LINE__,
"Memory allocation failed");
}
// get the column number for the wavelength
fits_get_colnum (s_models, CASEINSEN, "WAV_NM", &colnum1, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"create_interp_ftable: "
"Could not determine column %s in "
" table %s", "WAV_NM", spectral_models_file);
}
// read the wavelength
fits_read_col (s_models, TDOUBLE, colnum1, 1, 1, nrows, NULL, sed_wavs,
&anynul, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"load_SED_from_fitsext: "
"Could not read content of WAVELENGTH column "
" from BINARY table %s", spectral_models_file);
}
// get the column number for the flux
fits_get_colnum (s_models, CASEINSEN, "FLUX", &colnum2, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"create_interp_ftable: "
"Could not determine column %s in "
" table %s", "FLUX", spectral_models_file);
}
// read the flux column
fits_read_col (s_models, TDOUBLE, colnum2, 1, 1, nrows, NULL, sed_flux,
&anynul, &f_status);
if (f_status)
{
ffrprt (stderr, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"load_SED_from_fitsext: "
"Could not read content of FLUX column "
" from BINARY table %s", spectral_models_file);
}
// transfer the vector and length information
// to the SED object
sed->npoints = nrows;
sed->wavelength = sed_wavs ;
sed->flux = sed_flux;
// allocate some structures for the interpolator
sed->interp = gsl_interp_alloc (SMODEL_INTERP_TYPE, (size_t)sed->npoints );
sed->accel = gsl_interp_accel_alloc ();
// initialize the iterpolator
gsl_interp_init (sed->interp, sed->wavelength, sed->flux, (size_t)sed->npoints);
// return the energy distribution
return sed;
}
int
main (int argc, char *argv[])
{
char *opt;
char aper_file[MAXCHAR];
char aper_file_path[MAXCHAR];
char conf_file[MAXCHAR];
char conf_file_path[MAXCHAR];
char grism_file[MAXCHAR];
char grism_file_path[MAXCHAR];
char PET_file[MAXCHAR];
char PET_file_path[MAXCHAR];
// char outputroot[MAXCHAR];
// char outputroot_path[MAXCHAR];
char STP_file[MAXCHAR];
char STP_file_path[MAXCHAR];
// char output_path[MAXCHAR];
aperture_conf *conf;
object **oblist;
observation *obs;
ap_pixel *PET;
int index, i;
char label[MAXCHAR];
fitsfile *PET_ptr, *STP_ptr;
int f_status = 0;
int aperID, beamID, objindex;
FITScards *cards;
FITScards *xymin_cards;
gsl_matrix *rstamp;
drzstamp *drzstmp;
drzstamp_dim dim;
int rectified = 0;
//int drizzled = 0;
int drizzle=0;
int drzstamp=0;
int for_grism=0;
d_point stp_min;
if ((argc < 3) || (opt = get_online_option ("help", argc, argv)))
{
fprintf (stdout,
"ST-ECF European Coordinating Facility\n"
"aXe_STAMPS Version %s:\n"
" Task that generates some Postscript stamp images from the\n"
" content of a Pixel Extraction Table (PET)\n"
" The trace is overplotted and is generated from the group\n"
" of pixels in the PET which have the smallest projected distance\n"
" to the trace in the PET. No analytical a-priori trace function \n"
" is used.\n"
"\n"
"Usage:\n"
" aXe_STAMPS g/prism_filename configuration_filename [options]\n"
"\n"
"Options:\n"
" -rectified - produces rectified stamp image following the\n"
" direction of the extraction process\n"
" -drz - use $AXE_DRIZZLE_PATH to locate the grism-, OAF-\n"
" and PET-files instead of $AXE_IMAGE/OUTPUT_PATH\n"
" -in_AF=[string] - overwrite the automatically generated name\n"
" of the input aperture file\n"
" -in_PET=[string] - overwrite the automatically generated name\n"
" of the input PET file\n"
" -out_STP=[string] - overwrite the automatically generated name\n"
" of the output stamp FITS image\n"
"\n",RELEASE);
exit (1);
}
fprintf (stdout, "aXe_STAMPS: Starting...\n");
index = 0;
strcpy (grism_file, argv[++index]);
if ((opt = get_online_option ("drz", argc, argv))){
build_path (AXE_DRIZZLE_PATH, grism_file, grism_file_path);
drizzle=1;
}
else{
build_path (AXE_IMAGE_PATH, grism_file, grism_file_path);
drizzle=0;
}
strcpy (conf_file, argv[++index]);
build_path (AXE_CONFIG_PATH, conf_file, conf_file_path);
conf = get_aperture_descriptor (conf_file_path);
/* Determine where the various extensions are in the FITS file */
get_extension_numbers(grism_file_path, conf,conf->optkey1,conf->optval1);
/* Build aperture file name */
if ((opt = get_online_option("in_AF", argc, argv))){
/* get it */
strcpy (aper_file, opt);
strcpy (aper_file_path, opt);
}
else {
replace_file_extension (grism_file, aper_file, ".fits",
".OAF", conf->science_numext);
if (drizzle)
build_path (AXE_DRIZZLE_PATH, aper_file, aper_file_path);
else
build_path (AXE_OUTPUT_PATH, aper_file, aper_file_path);
}
if ((opt = get_online_option("in_PET", argc, argv))){
/* get it */
strcpy (PET_file, opt);
strcpy (PET_file_path, opt);
}
else{
/* Build object PET file name */
replace_file_extension (grism_file, PET_file, ".fits",
".PET.fits", conf->science_numext);
if (drizzle)
build_path (AXE_DRIZZLE_PATH, PET_file, PET_file_path);
else
build_path (AXE_OUTPUT_PATH, PET_file, PET_file_path);
}
if ( (opt = get_online_option ("out_STP", argc, argv)) )
{
strcpy (STP_file, opt);
// strcpy (STP_file_PATH, opt);
}
else
{
// replace_file_extension (PET_file, STP_file, ".PET.fits", ".STP.fits",-1);
replace_file_extension (grism_file, STP_file, ".fits", ".STP.fits",conf->science_numext);
}
if (drizzle)
build_path (AXE_DRIZZLE_PATH, STP_file, STP_file_path);
else
build_path (AXE_OUTPUT_PATH, STP_file, STP_file_path);
if ((opt=get_online_option("rectified",argc,argv)))
rectified = 1;
else if ((opt = get_online_option ("drzstamp", argc, argv)))
drzstamp=1;
// give feedback onto the screen:
// report on input and output
// and also on specific parameters
fprintf (stdout, "aXe_STAMPS: Input Image file name: %s\n",
grism_file_path);
fprintf (stdout, "aXe_STAMPS: Input Aperture file name: %s\n",
aper_file_path);
fprintf (stdout, "aXe_STAMPS: Input PET file name: %s\n",
PET_file_path);
fprintf (stdout, "aXe_STAMPS: Name of STP file : %s\n",
STP_file_path);
if (rectified)
fprintf (stdout, "aXe_STAMPS: Producing rectified stamp images.\n");
else if (drzstamp)
fprintf (stdout, "aXe_STAMPS: Producing drizzled stamp images.\n");
else
fprintf (stdout, "aXe_STAMPS: Producing trace stamp images.\n");
// Loading the object list
obs = load_dummy_observation ();
fprintf (stdout, "\naXe_STAMPS: Loading object aperture list...");
oblist = file_to_object_list_seq (aper_file_path, obs);
fprintf (stdout,"%d objects loaded.\n\n",object_list_size(oblist));
// Open the OPET file for reading
fits_open_file (&PET_ptr, PET_file_path, READONLY, &f_status);
if (f_status)
{
ffrprt (stdout, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_STAMPS: Could not open file: %s\n",
PET_file_path);
}
STP_ptr = create_FITSimage_opened (STP_file_path, 1);
i = 0;
if (oblist!=NULL)
{
while (1)
{
/* Get the PET for this object */
PET = get_ALL_from_next_in_PET(PET_ptr, &aperID, &beamID);
if ((aperID==-1) && (beamID==-1)) break;
fprintf (stdout, "aXe_STAMPS: BEAM %d%c.", aperID, BEAM(beamID));
objindex = find_object_in_object_list(oblist,aperID);
sprintf (label, "%s.%d%c.ps/CPS", STP_file_path,
oblist[objindex]->ID, BEAM (oblist[objindex]->beams[beamID].ID));
// determine the minimum in x and y
stp_min.x = -1.0;
stp_min.y = -1.0;
// special treatment for FORS2: dirzzled stamp images
if (drzstamp)
{
for_grism = check_for_grism (conf_file_path, beamID);
if (!for_grism)
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_STAMPS: Drizzled stamp images are not\n"
"supported for prism images. Please choose a different option!\n");
// get the dimensions of the drizzled stamp
dim = get_stamp_dim(PET, oblist[objindex]->beams[beamID].width, conf, beamID, &stp_min);
// fill the drzstamp structure (counts plus weight matrix)
drzstmp = drizzled_stamp_img (PET,oblist[objindex]->beams[beamID].width,
oblist[objindex]->beams[beamID].orient, dim);
// does this make sense
interpolate_over_NaN (drzstmp->counts);
// give the extension name and store the counts
sprintf (label, "BEAM_%d%c",oblist[objindex]->ID, BEAM (oblist[objindex]->beams[beamID].ID));
gsl_to_FITSimage_opened (drzstmp->counts, STP_ptr ,0,label);
// in case that the stamp is no dummy, make and store the WCS header
if (dim.resolution)
{
cards = get_WCS_FITScards(dim.xstart*dim.resolution, dim.resolution, dim.ystart);
put_FITS_cards_opened(STP_ptr,cards);
free_FITScards(cards);
}
// make and store the default header
cards = beam_to_FITScards(oblist[objindex],beamID);
xymin_cards = stpmin_to_FITScards(stp_min);
put_FITS_cards_opened(STP_ptr,cards);
put_FITS_cards_opened(STP_ptr,xymin_cards);
free_FITScards(cards);
free_FITScards(xymin_cards);
// give the extension name and store the weight image
sprintf (label, "WEIG_%d%c",oblist[objindex]->ID, BEAM (oblist[objindex]->beams[beamID].ID));
gsl_to_FITSimage_opened (drzstmp->weight, STP_ptr ,0,label);
// in case that the stamp is no dummy, make and store the WCS header
if (dim.resolution)
{
cards = get_WCS_FITScards(dim.xstart*dim.resolution, dim.resolution, dim.ystart);
put_FITS_cards_opened(STP_ptr,cards);
free_FITScards(cards);
}
// make and store the default header
cards = beam_to_FITScards(oblist[objindex],beamID);
xymin_cards = stpmin_to_FITScards(stp_min);
put_FITS_cards_opened(STP_ptr,cards);
put_FITS_cards_opened(STP_ptr,xymin_cards);
free_FITScards(cards);
free_FITScards(xymin_cards);
// free the structure with the count and weight matrix
free_drzstamp(drzstmp);
}
else
{
if (rectified)
{
rstamp = rectified_stamp_img (PET,oblist[objindex]->beams[beamID].width, &stp_min);
}
else
{
rstamp = stamp_img (PET,oblist[objindex]->beams[beamID].width, &stp_min);
}
sprintf (label, "BEAM_%d%c",oblist[objindex]->ID, BEAM (oblist[objindex]->beams[beamID].ID));
interpolate_over_NaN (rstamp);
gsl_to_FITSimage_opened (rstamp, STP_ptr ,0,label);
cards = beam_to_FITScards(oblist[objindex],beamID);
xymin_cards = stpmin_to_FITScards(stp_min);
put_FITS_cards_opened(STP_ptr,cards);
put_FITS_cards_opened(STP_ptr,xymin_cards);
free_FITScards(cards);
free_FITScards(xymin_cards);
free_stamp_img(rstamp);
}
if (PET!=NULL)
free(PET);
fprintf (stdout, " Done.\n");
i++;
}
}
if (oblist!=NULL) free_oblist (oblist);
fits_close_file (STP_ptr, &f_status);
if (f_status)
{
ffrprt (stdout, f_status);
aXe_message (aXe_M_FATAL, __FILE__, __LINE__,
"aXe_STAMPS: Could not" " close STP file: %s\n", STP_file_path);
}
fprintf (stdout, "aXe_STAMPS: Done...\n");
/* Copy the header info from the grism image */
{
FITScards *cards;
cards = get_FITS_cards (PET_file_path, 1);
put_FITS_cards(STP_file_path,1,cards);
free_FITScards(cards);
}
exit (0);
}
