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);
}
int
main (int argc, char *argv[])
{
char *opt;
char grism_image[MAXCHAR];
char grism_image_path[MAXCHAR];
char sex_catalog[MAXCHAR];
char sex_catalog_path[MAXCHAR];
char aper_file[MAXCHAR];
char aper_file_path[MAXCHAR];
char conf_file[MAXCHAR];
char conf_file_path[MAXCHAR];
float mmag_extract, mmag_mark, mfwhm, dmag;
int leaveout_ignored = 1;
int auto_reorient = 1;
int no_orient = 0;
int slitless_geom=0;
int num;
char ext[MAXCHAR];
double lambda_mark=0.0;
int bck_mode=0;
aperture_conf *conf;
SexObject **os;
object **oblist;
observation *obs;
if ((argc < 3) || (opt = get_online_option ("help", argc, argv)))
{
fprintf (stdout,
"ST-ECF European Coordinating Facility\n"
"aXe_GOL2AF Version %s:\n"
" aXe task to create an Object Aperture File (OAF)\n"
" or a Background Aperture File (BAF) (-bck option) using an\n"
" input Sextractor Grism Object List (GOL).\n"
" The AF files contain information about each object (aperture)\n"
" and information about the various beams (orders) in each of \n"
" these apertures. These are simple text files which can be\n"
" edited by hand. The IGNORE keywords can be set to 1 if a\n"
" particular beam (order) is to be ignored during the extraction\n"
" process. The MMAG_EXTRACT and MMAG_MARK keyword of each beam\n"
" listed in the aXe configuration file determine if a particluar\n "
" beam is flagged to be extracted or completely ignored.\n"
" The -dmag switch can be used to adjust these. See the aXe manual\n"
" for more details. An extraction width multiplicative factor can\n"
" be set with the -mfwhm option (e.g. to generate BAF containing\n"
" broader apertures).\n"
" By default, when the extraction angle is too close to the\n"
" dispersion direction, 90 degrees are added to the extraction\n"
" angle. This can be overwritten by using the -no_auto_orient\n"
" online parameter.\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_GOL2AF [g/prism image filename] [aXe filename] [options]\n"
"\n"
"Options:\n"
" -bck - to generate a BAF instead of an OAF file\n"
" -SCI_hdu=[integer] - overwrite the default from the \n"
" configuration file \n"
" -mfwhm=[float] - an extraction width multiplicative factor.\n"
" -exclude_faint - do not even list faint object in the result.\n"
" -out_AF=[string] - overwrites the default output aper filename.\n"
" -in_GOL=[string] - overwrites the default input catalog name.\n"
" -auto_orient=[0/1] - set to 0 to disable the automatic extraction\n"
" orientation.\n"
" -no_orient - disable tilted extraction (vertical\n"
" extraction only).\n"
" -dmag=[float] - A number to add to the MMAG_EXTRACT and\n"
" MMAG_MARK values.\n"
"\n"
"Example: ./aXe_GOL2AF slim_grism.fits -bck -dmag=2 -mfwhm=2\n"
"\n",RELEASE);
exit (1);
}
fprintf (stdout, "aXe_GOL2AF: Starting...\n");
/* Get the Grism/Prism image name */
strcpy (grism_image, argv[1]);
build_path (AXE_IMAGE_PATH, grism_image, grism_image_path);
/* Get the name of the configuration file */
strcpy (conf_file, argv[2]);
build_path (AXE_CONFIG_PATH, conf_file, conf_file_path);
/* Read the configuration file */
conf = get_aperture_descriptor (conf_file_path);
/* Determine where the various extensions are in the FITS file */
get_extension_numbers(grism_image_path, conf,conf->optkey1,conf->optval1);
if ((opt = get_online_option ("SCI_hdu", argc, argv)))
{
char str[MAXCHAR];
strcpy(str,opt);
conf->science_numext = atoi(str);
}
/* Get or set up the name of the output Aperture File */
if ((opt = get_online_option ("out_AF", argc, argv)))
{
/* get it */
strcpy (aper_file, opt);
strcpy (aper_file_path, opt);
}
else
{
/* set the name automatically */
/* Get the name of the aperture file type, OAF or BAF */
if ((opt=get_online_option ("bck",argc,argv)))
{
strcpy (ext,".BAF");
bck_mode=1;
}
else
{
strcpy (ext,".OAF");
}
strcpy (aper_file, argv[1]);
replace_file_extension (grism_image, aper_file, ".fits", ext,
conf->science_numext);
build_path (AXE_OUTPUT_PATH, aper_file, aper_file_path);
}
/* Set the option extraction width multiplicative factor */
if ((opt = get_online_option ("mfwhm", argc, argv)))
{
{
/*char str[MAXCHAR];
strcpy (str, opt);
sscanf (str, "%f", &mfwhm);*/
mfwhm = atof(opt);
}
}
else
{
mfwhm = 1.0;
}
if ((opt = get_online_option ("dmag", argc, argv)))
{
{
/*char str[MAXCHAR];
strcpy (str, opt);
sscanf (str, "%f", &mfwhm);*/
dmag = atof(opt);
}
}
else
{
dmag = 0.0;
}
/* Set the option to include object that are too faint into the output
aperture file.
*/
if ((opt = get_online_option ("exclude_faint", argc, argv)))
{
leaveout_ignored = 1;
}
else
{
leaveout_ignored = 0;
}
/* Set the auto orientation mode for extraction on or off, default is on (=1)
if ((opt = get_online_option ("auto_orient",argc,argv)))
{
if (!atof(opt))
auto_reorient = 0;
}
else
{
auto_reorient = 1;
}
*/
// set the flag for using slitless geometry,
// to say extraction parameters optimized for
// slitless geometry
if ((opt = get_online_option ("slitless_geom",argc,argv)))
if (!atof(opt))
//slitless_geom = 0;
auto_reorient = 0;
else
//slitless_geom = 1;
auto_reorient = 1;
/* Set the option to disbale tilted extraction */
if ((opt = get_online_option ("orient", argc, argv)))
{
if (!atof(opt))
auto_reorient = 2;
}
/* Get or generate the name of the sextractor catalog to read */
if ((opt = get_online_option ("in_GOL", argc, argv)))
{
strcpy (sex_catalog, opt);
strcpy (sex_catalog_path, opt);
}
else
{
strcpy (sex_catalog, argv[1]);
replace_file_extension (grism_image, sex_catalog, ".fits", ".cat",
conf->science_numext);
build_path (AXE_OUTPUT_PATH, sex_catalog, sex_catalog_path);
}
if ((opt = get_online_option ("lambda_mark", argc, argv)))
{
lambda_mark = atof(opt);
}
else{
lambda_mark = 800.0;
}
// check the configuration file for the smoothin keywords
if (!check_conf_for_slitlessgeom(conf, auto_reorient))
//if (!check_conf_for_slitlessgeom(conf, slitless_geom))
aXe_message(aXe_M_FATAL, __FILE__, __LINE__,
"aXe_GOL2AF: Either the configuration file %s does not contain\n"
"the necessary keywords for the slitless geometry: POBJSIZE,\n"
"or this keyword has an unreasonable value < 0.0!\n",
conf_file_path);
fprintf (stdout,
"aXe_GOL2AF: Main configuration file name: %s\n",
conf_file_path);
fprintf (stdout,
"aXe_GOL2AF: Input data file name: %s\n",
grism_image_path);
fprintf (stdout,
"aXe_GOL2AF: SCI extension number: %d\n",
conf->science_numext);
fprintf (stdout,
"aXe_GOL2AF: Input grism object list (GOL): %s\n",
sex_catalog_path);
fprintf (stdout,
"aXe_GOL2AF: Output aperture file name: %s\n",
aper_file_path);
fprintf (stdout,
"aXe_GOL2AF: FWHM multiplicative factor: %f\n",
mfwhm);
fprintf (stdout,
"aXe_GOL2AF: Dmag adjustment: %f\n",
dmag);
if (leaveout_ignored)
fprintf (stdout,
"aXe_GOL2AF: Ignored object will not "
"be included in the output aperture file\n");
if (!leaveout_ignored)
fprintf (stdout,
"aXe_GOL2AF: Ignored object will be "
"included in the output aperture file\n");
if (auto_reorient != 2)
fprintf (stdout,
"aXe_GOL2AF: Tilted extraction will be performed.\n");
if (auto_reorient == 0)
fprintf (stdout,
"aXe_GOL2AF: The extraction geometry follows the object\n");
if (auto_reorient == 1)
//if (slitless_geom)
fprintf (stdout,
"aXe_GOL2AF: Extraction geometry is optimized for slitless spectroscopy.\n");
//else
// fprintf (stdout,
// "aXe_GOL2AF: The extraction geometry follows the object, but may switch.\n");
if (auto_reorient==2)
fprintf (stdout,
"aXe_GOL2AF: NO tilted extraction will be performed (e.g. vertical only).\n");
fprintf (stdout,
"aXe_GOL2AF: Wavelength for object selection [nm]: %f\n",
lambda_mark);
fprintf(stdout,"\n\n");
// extend the beams when creating
// BAF's
if (bck_mode)
extend_config_beams(conf);
fprintf (stdout, "aXe_GOL2AF: Loading object list...");
os = get_SexObject_from_catalog (sex_catalog_path, lambda_mark);
fprintf (stdout, "Done.\n");fflush(stdout);
fprintf (stdout, "aXe_GOL2AF: Reading image...");
obs = load_empty_image (grism_image_path, conf->science_numext);
fprintf (stdout, "Done.\n");fflush(stdout);
fprintf (stdout, "aXe_GOL2AF: Generating aperture list...");
//if (!slitless_geom)
//use the old, aXe-1.6 code
//oblist = SexObjects_to_oblist(os, obs, conf, conf_file_path, mfwhm, dmag,
// auto_reorient, bck_mode);
// else
// use the new aXe-1.7 code
oblist = SexObjects_to_oblistII(os, obs, conf, conf_file_path, mfwhm, dmag, auto_reorient, bck_mode);
fprintf (stdout, "Done.\n");fflush(stdout);
fprintf (stdout, "aXe_GOL2AF: Writing aperture file...");fflush(stdout);
num = object_list_to_file (oblist, aper_file_path, leaveout_ignored);
fprintf (stdout, "%d beams written.\n", num);
free_SexObjects (os);
free_oblist (oblist);
fprintf (stdout, "aXe_GOL2AF: Done...\n");
exit (0);
}
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 specmod_file[MAXCHAR];
char specmod_file_path[MAXCHAR];
char objmod_file[MAXCHAR];
char objmod_file_path[MAXCHAR];
aperture_conf *conf;
int index;
double lambda_psf=0.0;
observation *obs;
if ((argc < 3) || (opt = get_online_option ("help", argc, argv)))
{
fprintf (stdout,
"Usage:\n"
" aXe_DISPIMAGE g/prism_filename configuration_filename"
"\n"
"Options:\n"
" -in_AF=[string] - overwrite the automatically generated name\n"
" of the input aperture file\n"
" -model_spectra=[string] - input model spectra"
" -model_images=[string] - input model images"
" -lambda_psf=[float] - lambda at which psf was measured"
"\n",RELEASE);
exit (1);
}
fprintf (stdout, "aXe_DISPIMAGE: Starting...\n");
index = 0;
strcpy (grism_file, argv[++index]);
build_path (AXE_IMAGE_PATH, grism_file, grism_file_path);
strcpy (conf_file, argv[++index]);
build_path (AXE_CONFIG_PATH, conf_file, conf_file_path);
conf = get_aperture_descriptor (conf_file_path);
get_extension_numbers(grism_file_path, conf,conf->optkey1,conf->optval1);
/* Get or set up the name of the output Aperture File */
if ((opt = get_online_option ("in_AF", argc, argv)))
{
/* get it */
strcpy (aper_file, opt);
strcpy (aper_file_path, opt);
}
else {
/* Build aperture file name */
replace_file_extension (grism_file, aper_file, ".fits",
".OAF", conf->science_numext);
build_path (AXE_OUTPUT_PATH, aper_file, aper_file_path);
}
// determine the wavelength
// the object extend was determined at
if ((opt = get_online_option ("lambda_psf", argc, argv)))
lambda_psf = atof(opt);
else
lambda_psf = 800.0;
// check whether a name for the spectral
// models file is given
if ((opt = get_online_option ("model_spectra", argc, argv)))
{
// get and set up the filename
strcpy (specmod_file, opt);
build_path (AXE_IMAGE_PATH, specmod_file, specmod_file_path);
}
else
{
strcpy (specmod_file, "");
strcpy (specmod_file_path, "");
}
// check whether a name for the images
// models file is given
if ((opt = get_online_option ("model_images", argc, argv)))
{
// get and set up the filename
strcpy (objmod_file, opt);
build_path (AXE_IMAGE_PATH, objmod_file, objmod_file_path);
}
else
{
strcpy (objmod_file, "");
strcpy (objmod_file_path, "");
}
fprintf (stdout, "aXe_DISPIMAGE: grism image file name: %s\n", grism_file_path);
fprintf (stdout, "aXe_DISPIMAGE: Input Aperture file name: %s\n", aper_file_path);
fprintf (stdout, "aXe_DISPIMAGE: Using spectral models in table: %s\n", specmod_file_path);
fprintf (stdout, "aXe_DISPIMAGE: Using direct emission objects in image: %s\n", objmod_file_path);
fprintf (stdout, "aXe_DISPIMAGE: Object parameters determined at %fnm\n", lambda_psf);
fprintf (stdout, "aXe_DISPIMAGE: ");
obs = load_sci_image (grism_file_path, conf->science_numext);
compute_disp(grism_file_path, aper_file_path, conf_file_path,
specmod_file_path, objmod_file_path, lambda_psf, obs);
free_observation(obs);
free_aperture_conf(conf);
fprintf (stdout, "aXe_DISPIMAGE: Done...\n");
exit (0);
}
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);
}
