/* A convenience method to populate MarkersReference from MarkerData **/
void MarkersReference::populateFromMarkerData(const MarkerData& aMarkerData)
{
const Array<std::string> &tempNames = aMarkerData.getMarkerNames();
int nm = tempNames.getSize();
// empty any lingering names and weights
_markerNames.clear();
_weights.clear();
// pre-allocate arrays to the number of markers in the file with default weightings
_markerNames.assign(nm, "");
_weights.assign(nm, get_default_weight());
for (int i = 0; i < nm; i++) {
const std::string &name = tempNames[i];
_markerNames[i] = name;
}
// Names must be assigned before weights can be updated
updateInternalWeights();
}
void MarkersReference::updateInternalWeights() const
{
// if weights are not being changed, do not rebuild list of weights.
if (isObjectUpToDateWithProperties())
return;
// Begin by assigning default weight to each. Markers that do not have a
// weight specified in the marker_weights property use the default weight.
_weights.assign(getNumRefs(), get_default_weight());
// Next fill in the marker weights that were specified in the
// marker_weights property
int wix = -1;
int ix = 0;
// Build flat lists of marker weights in the same order as the marker names
for (const std::string &name : _markerNames) {
wix = get_marker_weights().getIndex(name, wix);
// Associate user weights (as specified in the marker_weights property)
// with the corresponding marker by order of marker names
if (wix >= 0)
_weights[ix++] = get_marker_weights()[wix].getWeight();
}
}
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);
}
