27#include <cxmessages.h>
29#include <cpl_recipe.h>
30#include <cpl_plugininfo.h>
31#include <cpl_parameterlist.h>
32#include <cpl_frameset.h>
34#include <cpl_errorstate.h>
36#include <irplib_sdp_spectrum.h>
42#include "gifiberutils.h"
43#include "gislitgeometry.h"
49#include "gitransmission.h"
50#include "girebinning.h"
51#include "gisgcalibration.h"
52#include "giastrometry.h"
54#include "gimessages.h"
58const char *sciqcpar[] = {
59 GIALIAS_WLSTART, GIALIAS_WLEND,
60 GIALIAS_WLSTEP, GIALIAS_QCAIR, GIALIAS_QCFWHM,
61 GIALIAS_QCNFIB, GIALIAS_QCNFIBSCI, GIALIAS_QCNFIBSKY,
62 GIALIAS_QCMEANRED, GIALIAS_QCNSATSCI, GIALIAS_QCSNR,
63 GIALIAS_QCMAG, GIALIAS_QCDLTTEMP, GIALIAS_QCDLTTIME,
67static cxint giscience(cpl_parameterlist*, cpl_frameset*);
69static cxint _giraffe_make_sdp_spectra(
const cxchar* flux_filename,
70 const cxchar* err_filename,
72 cpl_frameset* allframes,
73 const cpl_parameterlist* parlist,
74 const cxchar* recipe_id);
76const cxdouble saturation = 60000.;
82 static void replace_spaces_with_underscores(
char *str)
85 for (
int i = 0; str[i] !=
'\0'; i++) {
98giscience_create(cpl_plugin* plugin)
101 cpl_recipe* recipe = (cpl_recipe*)plugin;
103 cpl_parameter* p = NULL;
106 giraffe_error_init();
115 recipe->parameters = cpl_parameterlist_new();
116 cx_assert(recipe->parameters != NULL);
145 p = cpl_parameter_new_value(
"giraffe.siwc.apply",
147 "Enable simultaneous wavelength calibration "
152 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI,
"siwc-apply");
153 cpl_parameterlist_append(recipe->parameters, p);
163 p = cpl_parameter_new_value(
"giraffe.sdp.format.generate",
165 "TRUE if additional files should be generated"
166 " in Science Data Product (SDP) format.",
170 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI,
"generate-SDP-format");
171 cpl_parameterlist_append(recipe->parameters, p);
173 p = cpl_parameter_new_value(
"giraffe.sdp.nassoc.keys",
175 "Sets the number of dummy (empty) ASSONi,"
176 " ASSOCi and ASSOMi keywords to create.",
180 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI,
181 "dummy-association-keys");
182 cpl_parameterlist_append(recipe->parameters, p);
194giscience_exec(cpl_plugin* plugin)
197 cpl_errorstate prev_state;
199 cpl_recipe* recipe = (cpl_recipe*)plugin;
202 cx_assert(recipe->parameters != NULL);
203 cx_assert(recipe->frames != NULL);
205 prev_state = cpl_errorstate_get();
206 result = giscience(recipe->parameters, recipe->frames);
208 cpl_errorstate_dump(prev_state, CPL_FALSE, cpl_errorstate_dump_one);
215giscience_destroy(cpl_plugin* plugin)
218 cpl_recipe* recipe = (cpl_recipe*)plugin;
227 cpl_parameterlist_delete(recipe->parameters);
229 giraffe_error_clear();
241giscience(cpl_parameterlist* config, cpl_frameset* set)
244 const cxchar*
const _id =
"giscience";
247 const cxchar* filename = NULL;
250 cxbool calsim = FALSE;
252 cxbool gensdp = FALSE;
253 cxint nassoc_keys = 0;
254 cxchar* flux_filename = NULL;
255 cxchar* err_filename = NULL;
262 cxdouble exptime = 0.;
264 cx_slist* slist = NULL;
266 cpl_propertylist* properties = NULL;
268 cpl_matrix* biasareas = NULL;
270 cpl_frame* science_frame = NULL;
271 cpl_frame* mbias_frame = NULL;
272 cpl_frame* mdark_frame = NULL;
273 cpl_frame* bpixel_frame = NULL;
274 cpl_frame* slight_frame = NULL;
275 cpl_frame* locy_frame = NULL;
276 cpl_frame* locw_frame = NULL;
277 cpl_frame* psfdata_frame = NULL;
278 cpl_frame* grating_frame = NULL;
279 cpl_frame* linemask_frame = NULL;
280 cpl_frame* slit_frame = NULL;
281 cpl_frame* wcal_frame = NULL;
282 cpl_frame* rscience_frame = NULL;
283 cpl_frame* sext_frame = NULL;
284 cpl_frame* rbin_frame = NULL;
286 cpl_parameter* p = NULL;
288 GiImage* mbias = NULL;
289 GiImage* mdark = NULL;
290 GiImage* bpixel = NULL;
291 GiImage* slight = NULL;
292 GiImage* sscience = NULL;
293 GiImage* rscience = NULL;
295 GiTable* fibers = NULL;
296 GiTable* slitgeometry = NULL;
297 GiTable* grating = NULL;
298 GiTable* wcalcoeff = NULL;
300 GiLocalization* localization = NULL;
301 GiExtraction* extraction = NULL;
302 GiRebinning* rebinning = NULL;
304 GiBiasConfig* bias_config = NULL;
305 GiExtractConfig* extract_config = NULL;
306 GiFlatConfig* flat_config = NULL;
307 GiRebinConfig* rebin_config = NULL;
309 GiInstrumentMode mode;
311 GiRecipeInfo info = {(cxchar*)_id, 1, NULL, config};
313 GiGroupInfo groups[] = {
314 {GIFRAME_SCIENCE, CPL_FRAME_GROUP_RAW},
315 {GIFRAME_BADPIXEL_MAP, CPL_FRAME_GROUP_CALIB},
316 {GIFRAME_BIAS_MASTER, CPL_FRAME_GROUP_CALIB},
317 {GIFRAME_DARK_MASTER, CPL_FRAME_GROUP_CALIB},
318 {GIFRAME_FIBER_FLAT_EXTSPECTRA, CPL_FRAME_GROUP_CALIB},
319 {GIFRAME_FIBER_FLAT_EXTERRORS, CPL_FRAME_GROUP_CALIB},
320 {GIFRAME_SCATTERED_LIGHT_MODEL, CPL_FRAME_GROUP_CALIB},
321 {GIFRAME_LOCALIZATION_CENTROID, CPL_FRAME_GROUP_CALIB},
322 {GIFRAME_LOCALIZATION_WIDTH, CPL_FRAME_GROUP_CALIB},
323 {GIFRAME_PSF_CENTROID, CPL_FRAME_GROUP_CALIB},
324 {GIFRAME_PSF_WIDTH, CPL_FRAME_GROUP_CALIB},
325 {GIFRAME_PSF_DATA, CPL_FRAME_GROUP_CALIB},
326 {GIFRAME_WAVELENGTH_SOLUTION, CPL_FRAME_GROUP_CALIB},
327 {GIFRAME_LINE_MASK, CPL_FRAME_GROUP_CALIB},
328 {GIFRAME_SLITSETUP, CPL_FRAME_GROUP_CALIB},
329 {GIFRAME_SLITMASTER, CPL_FRAME_GROUP_CALIB},
330 {GIFRAME_GRATING, CPL_FRAME_GROUP_CALIB},
331 {NULL, CPL_FRAME_GROUP_NONE}
337 cpl_msg_error(_id,
"Invalid parameter list! Aborting ...");
342 cpl_msg_error(_id,
"Invalid frame set! Aborting ...");
346 status = giraffe_frameset_set_groups(set, groups);
349 cpl_msg_error(_id,
"Setting frame group information failed!");
358 nscience = cpl_frameset_count_tags(set, GIFRAME_SCIENCE);
361 cpl_msg_error(_id,
"Too few (%ld) raw frames (%s) present in "
362 "frame set! Aborting ...", nscience, GIFRAME_SCIENCE);
366 locy_frame = cpl_frameset_find(set, GIFRAME_PSF_CENTROID);
368 if (locy_frame == NULL) {
370 locy_frame = cpl_frameset_find(set, GIFRAME_LOCALIZATION_CENTROID);
372 if (locy_frame == NULL) {
373 cpl_msg_info(_id,
"No master localization (centroid position) "
374 "present in frame set. Aborting ...");
380 locw_frame = cpl_frameset_find(set, GIFRAME_PSF_WIDTH);
382 if (locw_frame == NULL) {
384 locw_frame = cpl_frameset_find(set, GIFRAME_LOCALIZATION_WIDTH);
386 if (locw_frame == NULL) {
387 cpl_msg_info(_id,
"No master localization (spectrum width) "
388 "present in frame set. Aborting ...");
394 grating_frame = cpl_frameset_find(set, GIFRAME_GRATING);
396 if (!grating_frame) {
397 cpl_msg_error(_id,
"No grating data present in frame set. "
405 cpl_msg_error(_id,
"No slit geometry present in frame set. "
410 wcal_frame = cpl_frameset_find(set, GIFRAME_WAVELENGTH_SOLUTION);
413 cpl_msg_error(_id,
"No dispersion solution present in frame set. "
418 linemask_frame = cpl_frameset_find(set, GIFRAME_LINE_MASK);
420 if (!linemask_frame) {
421 cpl_msg_warning(_id,
"No reference line mask present in frame set.");
424 bpixel_frame = cpl_frameset_find(set, GIFRAME_BADPIXEL_MAP);
427 cpl_msg_info(_id,
"No bad pixel map present in frame set.");
430 mbias_frame = cpl_frameset_find(set, GIFRAME_BIAS_MASTER);
433 cpl_msg_info(_id,
"No master bias present in frame set.");
436 mdark_frame = cpl_frameset_find(set, GIFRAME_DARK_MASTER);
439 cpl_msg_info(_id,
"No master dark present in frame set.");
442 slight_frame = cpl_frameset_find(set, GIFRAME_SCATTERED_LIGHT_MODEL);
445 cpl_msg_info(_id,
"No scattered light model present in frame set.");
448 psfdata_frame = cpl_frameset_find(set, GIFRAME_PSF_DATA);
450 if (!psfdata_frame) {
451 cpl_msg_info(_id,
"No PSF profile parameters present in frame set.");
459 slist = cx_slist_new();
461 science_frame = cpl_frameset_find(set, GIFRAME_SCIENCE);
463 for (i = 0; i < nscience; i++) {
465 filename = cpl_frame_get_filename(science_frame);
473 cpl_msg_error(_id,
"Cannot load raw science frame from '%s'. "
474 "Aborting ...", filename);
481 cx_slist_push_back(slist, raw);
483 science_frame = cpl_frameset_find(set, NULL);
487 nscience = (cxint)cx_slist_size(slist);
488 sscience = cx_slist_pop_front(slist);
491 cx_assert(properties != NULL);
493 cpl_errorstate tempes = cpl_errorstate_get();
497 double *scipix = cpl_image_get_data_double(sciim);
498 if (scipix != NULL) {
499 const size_t nxy = (size_t)(cpl_image_get_size_x(sciim) *
500 cpl_image_get_size_y(sciim));
503 for (scii = 0; scii < nxy; scii++) {
504 if (scipix[scii] > saturation)
509 cpl_errorstate_set(tempes);
512 cpl_propertylist_update_int(properties, GIALIAS_QCNSATSCI, nsaturated);
521 cpl_msg_info(_id,
"Averaging science frames ...");
523 exptime = cpl_propertylist_get_double(properties, GIALIAS_EXPTIME);
525 for (i = 1; i < nscience; i++) {
527 cpl_propertylist* _properties;
529 GiImage* science = cx_slist_pop_front(slist);
536 cx_assert(_properties != NULL);
538 exptime += cpl_propertylist_get_double(_properties, GIALIAS_EXPTIME);
547 cx_assert(cx_slist_empty(slist));
548 cx_slist_delete(slist);
558 cpl_msg_info(_id,
"Updating stacked science image properties ...");
560 cpl_propertylist_set_double(properties, GIALIAS_EXPTIME,
563 cpl_propertylist_append_double(properties, GIALIAS_EXPTTOT, exptime);
564 cpl_propertylist_set_comment(properties, GIALIAS_EXPTTOT,
565 "Total exposure time of all frames "
568 cpl_propertylist_erase(properties, GIALIAS_TPLEXPNO);
572 cpl_propertylist_append_int(properties, GIALIAS_DATANCOM, nscience);
573 cpl_propertylist_set_comment(properties, GIALIAS_DATANCOM,
574 "Number of combined frames");
588 if (bias_config->method == GIBIAS_METHOD_MASTER ||
589 bias_config->method == GIBIAS_METHOD_ZMASTER) {
592 cpl_msg_error(_id,
"Missing master bias frame! Selected bias "
593 "removal method requires a master bias frame!");
601 filename = cpl_frame_get_filename(mbias_frame);
608 cpl_msg_error(_id,
"Cannot load master bias from '%s'. "
609 "Aborting ...", filename);
626 filename = cpl_frame_get_filename(bpixel_frame);
633 cpl_msg_error(_id,
"Cannot load bad pixel map from '%s'. "
634 "Aborting ...", filename);
675 cpl_msg_error(_id,
"Bias removal failed. Aborting ...");
680 if (bpixel != NULL) {
696 GiDarkConfig dark_config = {GIDARK_METHOD_ZMASTER, 0.};
699 cpl_msg_info(_id,
"Correcting for dark current ...");
701 filename = cpl_frame_get_filename(mdark_frame);
707 cpl_msg_error(_id,
"Cannot load master dark from '%s'. "
708 "Aborting ...", filename);
713 if (bpixel != NULL) {
725 cpl_msg_error(_id,
"Dark subtraction failed! Aborting ...");
733 if (bpixel != NULL) {
752 cpl_msg_info(_id,
"Writing pre-processed science image ...");
757 GIFRAME_SCIENCE_REDUCED,
758 CPL_FRAME_LEVEL_INTERMEDIATE,
761 if (rscience_frame == NULL) {
762 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
769 cpl_frameset_insert(set, rscience_frame);
776 science_frame = cpl_frameset_find(set, GIFRAME_SCIENCE);
778 cpl_msg_info(_id,
"Building fiber setup for frame '%s'.",
779 cpl_frame_get_filename(science_frame));
784 cpl_msg_error(_id,
"Cannot create fiber setup for frame '%s'! "
785 "Aborting ...", cpl_frame_get_filename(science_frame));
798 cpl_msg_info(_id,
"Fiber reference setup taken from localization "
799 "frame '%s'.", cpl_frame_get_filename(locy_frame));
806 localization = giraffe_localization_new();
808 filename = cpl_frame_get_filename(locy_frame);
815 cpl_msg_error(_id,
"Cannot load localization (centroid "
816 "position) frame from '%s'. Aborting ...",
819 giraffe_localization_destroy(localization);
833 filename = cpl_frame_get_filename(locw_frame);
840 cpl_msg_error(_id,
"Cannot load localization (spectrum width) "
841 "frame from '%s'. Aborting ...", filename);
843 giraffe_localization_destroy(localization);
863 filename = cpl_frame_get_filename(slight_frame);
870 cpl_msg_error(_id,
"Cannot load scattered light model from '%s'. "
871 "Aborting ...", filename);
875 giraffe_localization_destroy(localization);
894 if ((extract_config->emethod == GIEXTRACT_OPTIMAL) ||
895 (extract_config->emethod == GIEXTRACT_HORNE)) {
897 if (psfdata_frame == NULL) {
899 const cxchar* emethod =
"Optimal";
901 if (extract_config->emethod == GIEXTRACT_HORNE) {
905 cpl_msg_error(_id,
"%s spectrum extraction requires PSF "
906 "profile data. Aborting ...", emethod);
909 extract_config = NULL;
911 if (slight != NULL) {
916 giraffe_localization_destroy(localization);
935 filename = cpl_frame_get_filename(psfdata_frame);
938 localization->psf = giraffe_psfdata_new();
939 status = giraffe_psfdata_load(localization->psf, filename);
942 cpl_msg_error(_id,
"Cannot load PSF profile data frame from "
943 "'%s'. Aborting ...", filename);
946 extract_config = NULL;
948 if (slight != NULL) {
953 giraffe_localization_destroy(localization);
976 extraction = giraffe_extraction_new();
979 localization, bpixel, slight,
983 cpl_msg_error(_id,
"Spectrum extraction failed! Aborting ...");
985 giraffe_extraction_destroy(extraction);
990 giraffe_localization_destroy(localization);
1023 if (flat_config->load == TRUE) {
1025 cpl_frame* flat_frame = NULL;
1027 GiImage* flat = NULL;
1030 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTSPECTRA);
1032 if (flat_frame == NULL) {
1033 cpl_msg_error(_id,
"Missing flat field spectra frame!");
1037 giraffe_extraction_destroy(extraction);
1038 giraffe_localization_destroy(localization);
1048 filename = cpl_frame_get_filename(flat_frame);
1054 cpl_msg_error(_id,
"Cannot load flat field spectra from '%s'. "
1055 "Aborting ...", filename);
1061 giraffe_extraction_destroy(extraction);
1062 giraffe_localization_destroy(localization);
1072 if (flat_config->apply == TRUE) {
1074 GiImage* errors = NULL;
1077 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTERRORS);
1079 if (flat_frame == NULL) {
1080 cpl_msg_warning(_id,
"Missing flat field spectra errors "
1085 filename = cpl_frame_get_filename(flat_frame);
1091 cpl_msg_error(_id,
"Cannot load flat field spectra "
1092 "errors from '%s'. Aborting ...",
1100 giraffe_extraction_destroy(extraction);
1101 giraffe_localization_destroy(localization);
1113 cpl_msg_info(_id,
"Applying flat field correction ...");
1119 cpl_msg_error(_id,
"Flat field correction failed! "
1127 giraffe_extraction_destroy(extraction);
1128 giraffe_localization_destroy(localization);
1143 if (flat_config->transmission == TRUE) {
1145 const cxchar* _filename = cpl_frame_get_filename(flat_frame);
1147 GiTable* _fibers = NULL;
1150 cpl_msg_info(_id,
"Loading fiber setup for frame '%s'.",
1156 cpl_msg_error(_id,
"Cannot create fiber setup for "
1157 "frame '%s'! Aborting ...", _filename);
1163 giraffe_extraction_destroy(extraction);
1164 giraffe_localization_destroy(localization);
1174 cpl_msg_info(_id,
"Applying relative fiber transmission "
1177 status = giraffe_transmission_setup(fibers, _fibers);
1181 status = giraffe_transmission_apply(extraction, fibers);
1186 cpl_msg_error(_id,
"Relative transmission correction failed! "
1193 giraffe_extraction_destroy(extraction);
1194 giraffe_localization_destroy(localization);
1219 cpl_msg_info(_id,
"Writing extracted spectra ...");
1227 giraffe_qc_update_sci_props(extprop, fibers);
1231 GIFRAME_SCIENCE_EXTSPECTRA,
1232 CPL_FRAME_LEVEL_FINAL,
1235 if (sext_frame == NULL) {
1236 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1238 giraffe_extraction_destroy(extraction);
1239 giraffe_localization_destroy(localization);
1252 cpl_msg_error(_id,
"Cannot attach fiber setup to local file '%s'! "
1253 "Aborting ...", cpl_frame_get_filename(sext_frame));
1255 cpl_frame_delete(sext_frame);
1257 giraffe_extraction_destroy(extraction);
1258 giraffe_localization_destroy(localization);
1268 cpl_frameset_insert(set, sext_frame);
1276 giraffe_qc_update_sci_props(exterrprop, fibers);
1282 GIFRAME_SCIENCE_EXTERRORS,
1283 CPL_FRAME_LEVEL_FINAL,
1286 if (sext_frame == NULL) {
1287 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1289 giraffe_extraction_destroy(extraction);
1290 giraffe_localization_destroy(localization);
1303 cpl_msg_error(_id,
"Cannot attach fiber setup to local file '%s'! "
1304 "Aborting ...", cpl_frame_get_filename(sext_frame));
1306 cpl_frame_delete(sext_frame);
1308 giraffe_extraction_destroy(extraction);
1309 giraffe_localization_destroy(localization);
1319 cpl_frameset_insert(set, sext_frame);
1323 if (extraction->npixels != NULL) {
1327 giraffe_qc_update_sci_props(extpixprop, fibers);
1332 GIFRAME_SCIENCE_EXTPIXELS,
1333 CPL_FRAME_LEVEL_FINAL,
1336 if (sext_frame == NULL) {
1337 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1339 giraffe_extraction_destroy(extraction);
1340 giraffe_localization_destroy(localization);
1353 cpl_msg_error(_id,
"Cannot attach fiber setup to local file '%s'! "
1354 "Aborting ...", cpl_frame_get_filename(sext_frame));
1356 cpl_frame_delete(sext_frame);
1358 giraffe_extraction_destroy(extraction);
1359 giraffe_localization_destroy(localization);
1369 cpl_frameset_insert(set, sext_frame);
1378 GIFRAME_SCIENCE_EXTTRACE,
1379 CPL_FRAME_LEVEL_FINAL,
1382 if (sext_frame == NULL) {
1383 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1385 giraffe_extraction_destroy(extraction);
1386 giraffe_localization_destroy(localization);
1399 cpl_msg_error(_id,
"Cannot attach fiber setup to local file '%s'! "
1400 "Aborting ...", cpl_frame_get_filename(sext_frame));
1402 cpl_frame_delete(sext_frame);
1404 giraffe_extraction_destroy(extraction);
1405 giraffe_localization_destroy(localization);
1415 cpl_frameset_insert(set, sext_frame);
1419 if (extraction->model != NULL) {
1424 GIFRAME_SCIENCE_EXTMODEL,
1425 CPL_FRAME_LEVEL_FINAL,
1428 if (sext_frame == NULL) {
1429 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1431 giraffe_extraction_destroy(extraction);
1432 giraffe_localization_destroy(localization);
1445 cpl_msg_error(_id,
"Cannot attach fiber setup to local file '%s'! "
1446 "Aborting ...", cpl_frame_get_filename(sext_frame));
1448 cpl_frame_delete(sext_frame);
1450 giraffe_extraction_destroy(extraction);
1451 giraffe_localization_destroy(localization);
1461 cpl_frameset_insert(set, sext_frame);
1471 filename = (cxchar *)cpl_frame_get_filename(wcal_frame);
1473 tempes = cpl_errorstate_get();
1475 const char qcdltcopy[] =
"^(ESO INS TEMP53 VAL|MJD-OBS)$";
1476 cpl_propertylist * qcdltlist = cpl_propertylist_load_regexp(filename, 0,
1478 cpl_errorstate_set(tempes);
1484 cpl_msg_error(_id,
"Cannot load dispersion solution from "
1485 "'%s'. Aborting ...", filename);
1487 giraffe_extraction_destroy(extraction);
1488 giraffe_localization_destroy(localization);
1503 filename = (cxchar *)cpl_frame_get_filename(grating_frame);
1511 cpl_msg_error(_id,
"Cannot load grating data from '%s'. "
1512 "Aborting ...", filename);
1514 giraffe_extraction_destroy(extraction);
1515 giraffe_localization_destroy(localization);
1531 filename = (cxchar *)cpl_frame_get_filename(slit_frame);
1535 if (slitgeometry == NULL) {
1536 cpl_msg_error(_id,
"Cannot load slit geometry data from '%s'. "
1537 "Aborting ...", filename);
1541 giraffe_extraction_destroy(extraction);
1542 giraffe_localization_destroy(localization);
1560 cpl_msg_error(_id,
"Slit geometry data from '%s' is not "
1561 "applicable for current fiber setup! "
1562 "Aborting ...", filename);
1567 giraffe_extraction_destroy(extraction);
1568 giraffe_localization_destroy(localization);
1586 cpl_msg_info(_id,
"Spectrum rebinning");
1593 localization, grating, slitgeometry,
1594 wcalcoeff, rebin_config);
1597 cpl_msg_error(_id,
"Rebinning of science spectra failed! Aborting...");
1601 giraffe_extraction_destroy(extraction);
1602 giraffe_localization_destroy(localization);
1623 p = cpl_parameterlist_find(config,
"giraffe.siwc.apply");
1624 cx_assert(p != NULL);
1626 siwc = cpl_parameter_get_bool(p);
1630 cx_assert(properties != NULL);
1633 if (cpl_propertylist_has(properties, GIALIAS_STSCTAL) == TRUE) {
1634 calsim = cpl_propertylist_get_bool(properties, GIALIAS_STSCTAL);
1638 if ((siwc == TRUE) && (calsim == TRUE) && (linemask_frame != NULL)) {
1647 if (siwc_config == NULL) {
1654 giraffe_extraction_destroy(extraction);
1655 giraffe_localization_destroy(localization);
1669 filename = cpl_frame_get_filename(linemask_frame);
1674 cpl_msg_error(_id,
"Cannot load line reference mask from '%s'. "
1675 "Aborting ...", filename);
1685 giraffe_extraction_destroy(extraction);
1686 giraffe_localization_destroy(localization);
1702 linemask, siwc_config);
1705 cpl_msg_error(_id,
"Applying simultaneous wavelength "
1706 "calibration correction failed! Aborting...");
1716 giraffe_extraction_destroy(extraction);
1717 giraffe_localization_destroy(localization);
1741 localization, grating, slitgeometry,
1742 wcalcoeff, rebin_config);
1745 cpl_msg_error(_id,
"Rebinning of science spectra failed! "
1750 giraffe_extraction_destroy(extraction);
1751 giraffe_localization_destroy(localization);
1767 giraffe_extraction_destroy(extraction);
1770 giraffe_localization_destroy(localization);
1771 localization = NULL;
1774 rebin_config = NULL;
1791 cpl_msg_warning(_id,
"Missing observation time properties! "
1792 "Barycentric correction computation "
1799 cpl_msg_warning(_id,
"Missing telescope location properties! "
1800 "Barycentric correction computation "
1807 cpl_msg_warning(_id,
"Object positions are not available "
1808 "Barycentric correction computation "
1815 cpl_msg_error(_id,
"Barycentric correction computation "
1816 "failed! Aborting...");
1843 tempes = cpl_errorstate_get();
1855 double dlttemp = cpl_propertylist_get_double(rbprop,
"ESO INS TEMP53 VAL");
1856 dlttemp -= cpl_propertylist_get_double(qcdltlist,
"ESO INS TEMP53 VAL");
1858 double dltdate = cpl_propertylist_get_double(rbprop,
"MJD-OBS");
1859 dltdate -= cpl_propertylist_get_double(qcdltlist,
"MJD-OBS");
1861 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTEMP, dlttemp);
1862 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTIME, dltdate);
1865 cpl_errorstate_set(tempes);
1870 GIFRAME_SCIENCE_RBNSPECTRA,
1871 CPL_FRAME_LEVEL_FINAL,
1874 if (rbin_frame == NULL) {
1875 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1891 cpl_msg_error(_id,
"Cannot attach fiber setup to local "
1892 "file '%s'! Aborting ...",
1893 cpl_frame_get_filename(rbin_frame));
1902 cpl_frame_delete(rbin_frame);
1907 cpl_frameset_insert(set, rbin_frame);
1908 flux_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
1912 tempes = cpl_errorstate_get();
1924 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTEMP, dlttemp);
1925 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTIME, dltdate);
1930 cpl_errorstate_set(tempes);
1933 GIFRAME_SCIENCE_RBNERRORS,
1934 CPL_FRAME_LEVEL_FINAL,
1937 if (rbin_frame == NULL) {
1938 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
1947 cpl_free(flux_filename);
1955 cpl_msg_error(_id,
"Cannot attach fiber setup to local "
1956 "file '%s'! Aborting ...",
1957 cpl_frame_get_filename(rbin_frame));
1967 cpl_frame_delete(rbin_frame);
1968 cpl_free(flux_filename);
1973 cpl_frameset_insert(set, rbin_frame);
1974 err_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
1982 p = cpl_parameterlist_find(config,
"giraffe.sdp.format.generate");
1983 cx_assert(p != NULL);
1984 gensdp = cpl_parameter_get_bool(p);
1985 p = cpl_parameterlist_find(config,
"giraffe.sdp.nassoc.keys");
1986 cx_assert(p != NULL);
1987 nassoc_keys = cpl_parameter_get_int(p);
1990 if (mode == GIMODE_MEDUSA) {
1991 status = _giraffe_make_sdp_spectra(flux_filename, err_filename,
1992 nassoc_keys, set, config, _id);
1994 cpl_msg_error(_id,
"Failed to generate spectra in Science Data"
1995 " Product format.");
2005 cpl_free(flux_filename);
2006 cpl_free(err_filename);
2011 cpl_msg_warning(_id,
"Requested to generate SDP 1D spectra, but"
2012 " this is currently only supported for the MEDUSA"
2013 " mode. Skipping SDP generation.");
2016 cpl_free(flux_filename);
2017 cpl_free(err_filename);
2024 if (mode == GIMODE_IFU || mode == GIMODE_ARGUS) {
2026 cpl_frame* rimg_frame = NULL;
2028 GiFieldOfView* fov = NULL;
2030 GiFieldOfViewConfig* fov_config = NULL;
2032 GiFieldOfViewCubeFormat cube_format = GIFOV_FORMAT_ESO3D;
2037 cube_format = fov_config->format;
2040 cpl_msg_info(_id,
"Reconstructing image and data cube from rebinned "
2046 slitgeometry, fov_config);
2051 cpl_msg_warning(_id,
"No reconstructed image was built. "
2052 "Fiber list has no fiber position "
2056 cpl_msg_error(_id,
"Image reconstruction failed! Aborting...");
2086 GIFRAME_SCIENCE_RCSPECTRA,
2087 CPL_FRAME_LEVEL_FINAL,
2090 if (rimg_frame == NULL) {
2091 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
2105 cpl_frameset_insert(set, rimg_frame);
2113 GIFRAME_SCIENCE_RCERRORS,
2114 CPL_FRAME_LEVEL_FINAL,
2117 if (rimg_frame == NULL) {
2118 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
2132 cpl_frameset_insert(set, rimg_frame);
2137 if (cube_format == GIFOV_FORMAT_SINGLE) {
2141 if (fov->cubes.spectra != NULL) {
2143 cxint component = 0;
2149 properties = cpl_propertylist_duplicate(properties);
2154 CPL_FRAME_LEVEL_FINAL,
2160 cpl_propertylist_delete(properties);
2163 if (rimg_frame == NULL) {
2164 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
2176 slitgeometry = NULL;
2190 cpl_msg_error(_id,
"Cannot attach fiber setup to local "
2191 "file '%s'! Aborting ...",
2192 cpl_frame_get_filename(rimg_frame));
2194 cpl_frame_delete(rimg_frame);
2206 slitgeometry = NULL;
2217 cpl_frameset_insert(set, rimg_frame);
2223 if (fov->cubes.errors != NULL) {
2225 cxint component = 1;
2231 properties = cpl_propertylist_duplicate(properties);
2236 CPL_FRAME_LEVEL_FINAL,
2242 cpl_propertylist_delete(properties);
2245 if (rimg_frame == NULL) {
2246 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
2258 slitgeometry = NULL;
2272 cpl_msg_error(_id,
"Cannot attach fiber setup to local "
2273 "file '%s'! Aborting ...",
2274 cpl_frame_get_filename(rimg_frame));
2276 cpl_frame_delete(rimg_frame);
2288 slitgeometry = NULL;
2299 cpl_frameset_insert(set, rimg_frame);
2310 properties = cpl_propertylist_duplicate(properties);
2315 CPL_FRAME_LEVEL_FINAL,
2321 cpl_propertylist_delete(properties);
2324 if (rimg_frame == NULL) {
2325 cpl_msg_error(_id,
"Cannot create local file! Aborting ...");
2337 slitgeometry = NULL;
2351 cpl_msg_error(_id,
"Cannot attach fiber setup to local "
2352 "file '%s'! Aborting ...",
2353 cpl_frame_get_filename(rimg_frame));
2355 cpl_frame_delete(rimg_frame);
2367 slitgeometry = NULL;
2378 cpl_frameset_insert(set, rimg_frame);
2411cpl_plugin_get_info(cpl_pluginlist* list)
2414 cpl_recipe* recipe = cx_calloc(1,
sizeof *recipe);
2415 cpl_plugin* plugin = &recipe->interface;
2418 cpl_plugin_init(plugin,
2420 GIRAFFE_BINARY_VERSION,
2421 CPL_PLUGIN_TYPE_RECIPE,
2423 "Process a science observation.",
2424 "For detailed information please refer to the "
2425 "GIRAFFE pipeline user manual.\nIt is available at "
2426 "http://www.eso.org/pipelines.",
2434 cpl_pluginlist_append(list, plugin);
2443typedef struct _giraffe_lut_entry {
2444 const char* expmode;
2459static cpl_boolean _giraffe_lut_is_sorted(
const giraffe_lut_entry* lut,
2463 if (nentries < 2)
return CPL_TRUE;
2464 for (i = 0; i < nentries - 1; ++i) {
2465 if (strcmp(lut[i].expmode, lut[i+1].expmode) >= 0) {
2482static const giraffe_lut_entry* _giraffe_find_lut_entry(
const char* expmode)
2484 static giraffe_lut_entry lut[] = {
2489 {
"H379.", 25000, 0.2250, 20.0, 60},
2490 {
"H379.0", 25000, 0.2250, 20.0, 60},
2491 {
"H395.8", 22000, 0.1913, 21.1, 53},
2492 {
"H412.4", 30000, 0.1326, 22.3, 48},
2493 {
"H429.7", 23000, 0.1471, 23.5, 67},
2494 {
"H447.1", 20000, 0.0906, 24.9, 63},
2495 {
"H447.1A", 20000, 0.0906, 24.9, 63},
2496 {
"H447.1B", 31000, 0.1297, 23.5, 58},
2497 {
"H465.6", 23000, 0.1573, 22.4, 57},
2498 {
"H484.5", 19000, 0.1175, 23.5, 57},
2499 {
"H484.5A", 19000, 0.1175, 23.5, 57},
2500 {
"H484.5B", 33000, 0.0907, 24.6, 61},
2501 {
"H504.8", 22000, 0.1726, 25.2, 56},
2502 {
"H525.8", 17000, 0.1397, 25.8, 49},
2503 {
"H525.8A", 17000, 0.1397, 25.8, 49},
2504 {
"H525.8B", 29000, 0.2014, 26.4, 44},
2505 {
"H548.8", 20000, 0.2389, 26.9, 51},
2506 {
"H572.8", 27000, 0.1844, 27.5, 49},
2507 {
"H599.3", 18000, 0.1683, 28.3, 57},
2508 {
"H627.3", 24000, 0.1268, 29.0, 50},
2509 {
"H651.5", 17000, 0.1185, 30.0, 42},
2510 {
"H651.5A", 17000, 0.1185, 30.0, 42},
2511 {
"H651.5B", 35000, 0.1253, 31.5, 37},
2512 {
"H665.", 17000, 0.2076, 33.0, 45},
2513 {
"H665.0", 17000, 0.2076, 33.0, 45},
2514 {
"H679.7", 19000, 0.1621, 34.5, 51},
2515 {
"H710.5", 25000, 0.1495, 36.0, 48},
2516 {
"H737.", 16000, 0.1456, 37.5, 47},
2517 {
"H737.0", 16000, 0.1456, 37.5, 47},
2518 {
"H737.0A", 16000, 0.1456, 37.5, 47},
2519 {
"H737.0B", 35000, 0.1147, 39.5, 40},
2520 {
"H769.1", 19000, 0.2811, 41.8, 35},
2521 {
"H805.3", 14000, 0.2662, 42.4, 39},
2522 {
"H805.3A", 14000, 0.2662, 42.4, 39},
2523 {
"H805.3B", 25000, 0.2342, 42.9, 28},
2524 {
"H836.6", 16000, 0.2032, 43.3, 21},
2525 {
"H836.6A", 16000, 0.2032, 43.3, 21},
2526 {
"H836.6B", 34000, 0.1073, 43.7, 14},
2527 {
"H875.7", 18000, 0.2026, 44.3, 29},
2528 {
"H920.5", 12000, 0.1568, 44.9, 32},
2529 {
"H920.5A", 12000, 0.1568, 44.9, 32},
2530 {
"H920.5B", 24000, 0.2531, 45.9, 28},
2531 {
"L385.7", 7500, 0.3358, 58.0, 43},
2532 {
"L427.2", 6300, 0.2152, 61.1, 62},
2533 {
"L479.7", 7500, 0.1554, 71.0, 61},
2534 {
"L543.1", 5800, 0.2065, 82.1, 58},
2535 {
"L614.2", 6600, 0.1803, 79.0, 51},
2536 {
"L682.2", 8100, 0.1843, 74.0, 50},
2537 {
"L773.4", 5400, 0.1617, 94.0, 44},
2538 {
"L881.7", 6600, 0.1614, 119.0, 29}
2540 static const size_t nentries =
sizeof(lut) /
sizeof(giraffe_lut_entry);
2542 int high = (int)nentries - 1;
2544 assert(_giraffe_lut_is_sorted(lut, nentries));
2545 assert(expmode != NULL);
2549 int mid = (low + high) >> 1;
2550 int result = strcmp(expmode, lut[mid].expmode);
2553 }
else if (result < 0) {
2558 }
while (high >= low);
2568static double _giraffe_lookup_specres(
const char* expmode)
2570 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2571 if (entry == NULL)
return NAN;
2572 return entry->specres;
2581static double _giraffe_lookup_lamrms(
const char* expmode)
2583 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2584 if (entry == NULL)
return NAN;
2585 if (isnan(entry->lamrms) || isnan(entry->spec_length))
return NAN;
2586 return entry->lamrms * entry->spec_length / 4100.;
2595static double _giraffe_lookup_lamnlin(
const char* expmode)
2597 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2598 if (entry == NULL)
return -1;
2599 return entry->lamnlin;
2613static cpl_type _giraffe_calc_wave_type(
double crval2,
double crpix2,
2614 double cdelt2, cpl_size naxis2)
2616 static const double errfrac = 0.02;
2617 static const double single_precision_digits = 7;
2618 double lo = (1.0 - crpix2) * cdelt2;
2619 double hi = ((double)naxis2 - crpix2) * cdelt2;
2620 double maxwave = crval2 + (hi > lo ? hi : lo);
2621 double binfrac = (maxwave != 0.0) ? fabs(cdelt2 / maxwave) : 0.0;
2622 if (binfrac * errfrac < pow(10, -single_precision_digits)) {
2623 return CPL_TYPE_DOUBLE;
2625 return CPL_TYPE_FLOAT;
2639static cpl_boolean _giraffe_ancillary_data_available(
const char* filename,
2640 const GiTable* fibertable)
2644 const char** spectypes = NULL;
2646 assert(filename != NULL);
2648 cpl_error_ensure(tbl != NULL, cpl_error_get_code(),
return CPL_FALSE,
2649 "The fiber table is not available for '%s'.", filename);
2651 spectypes = cpl_table_get_data_string_const(tbl, GIALIAS_COLUMN_TYPE);
2652 cpl_error_ensure(spectypes != NULL, cpl_error_get_code(),
return CPL_FALSE,
2653 "Could not fetch the '%s' column from the fiber setup"
2654 " table in '%s'.", GIALIAS_COLUMN_TYPE, filename);
2660 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2661 if ((spectypes[i][0] !=
'\0') && (strcmp(spectypes[i],
"M") != 0)) {
2688static cpl_error_code _giraffe_make_ancillary_file(cpl_frameset* allframes,
2689 const char* outputfile,
2690 const char* infilename,
2691 const GiImage* fluximage,
2692 const GiTable* fibertable)
2694 cpl_error_code error = CPL_ERROR_NONE;
2696 cpl_frame* frame = NULL;
2698 GiImage* image = NULL;
2700 cpl_image* img = NULL;
2702 cpl_image* subimg = NULL;
2703 cpl_propertylist* comments = NULL;
2705 int* indices = NULL;
2706 const char** spectypes = NULL;
2708 assert(allframes != NULL);
2709 assert(outputfile != NULL);
2710 assert(infilename != NULL);
2712 cpl_error_ensure(srcimg != NULL && table != NULL && tbl != NULL,
2713 cpl_error_get_code(),
goto cleanup,
2714 "The image or table are not available for '%s'.",
2718 frame = cpl_frame_new();
2719 error |= cpl_frame_set_filename(frame, outputfile);
2720 error |= cpl_frame_set_tag(frame, GIALIAS_ASSO_PROCATG_VALUE);
2721 error |= cpl_frame_set_type(frame, CPL_FRAME_TYPE_IMAGE);
2722 error |= cpl_frame_set_group(frame, CPL_FRAME_GROUP_PRODUCT);
2723 error |= cpl_frame_set_level(frame, CPL_FRAME_LEVEL_FINAL);
2724 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2725 "Failed to setup a new output frame for '%s'.",
2734 error |= cpl_table_unselect_all(tbl);
2735 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2736 "Failed to unselect all entries in fiber setup table from"
2737 " '%s'.", infilename);
2738 cpl_table_or_selected_string(tbl, GIALIAS_COLUMN_TYPE, CPL_NOT_EQUAL_TO,
2740 cpl_table_and_selected_int(tbl, GIALIAS_COLUMN_RP, CPL_NOT_EQUAL_TO, -1);
2741 cpl_table_not_selected(tbl);
2742 error |= cpl_table_erase_selected(tbl);
2743 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2744 "Failed to erase selected entries in fiber setup table"
2745 " from '%s'.", infilename);
2749 ny = cpl_image_get_size_y(srcimg);
2751 cpl_table_get_nrow(tbl), ny);
2755 cpl_error_ensure(image != NULL && img != NULL && retcode == 0,
2756 cpl_error_get_code(),
goto cleanup,
2757 "Failed to create image for output file '%s'.",
2762 GIALIAS_ASSO_PROCATG_VALUE);
2763 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2764 "Could not update keyword '%s' for output file '%s'.",
2765 GIALIAS_PROCATG, outputfile);
2770 GIALIAS_PRODCATG_MOSSKY);
2771 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2772 "Could not update keyword '%s' for output file '%s'.",
2773 GIALIAS_PRODCATG, outputfile);
2778 const char* comments_to_remove[] = {
2779 " FITS (Flexible Image Transport System) format is defined in"
2781 " and Astrophysics', volume 376, page 359; bibcode: 2001A&A..."
2786 comments = cpl_propertylist_new();
2787 error |= cpl_propertylist_copy_property_regexp(comments, props,
2789 cpl_propertylist_erase_regexp(props,
"^COMMENT$", 0);
2790 for (ic = 0; ic < cpl_propertylist_get_size(comments); ++ic) {
2791 const char** cmnt_str;
2792 cpl_property* p = cpl_propertylist_get(comments, ic);
2793 for (cmnt_str = comments_to_remove; *cmnt_str != NULL; ++cmnt_str) {
2794 if (strcmp(cpl_property_get_string(p), *cmnt_str) == 0) {
2795 goto dont_add_comment;
2799 error |= cpl_propertylist_append_property(props, p);
2805 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2806 "Failed to cleanup comments in primary HDU for '%s'.",
2808 cpl_propertylist_delete(comments);
2814 indices = cpl_table_get_data_int(tbl, GIALIAS_COLUMN_INDEX);
2815 cpl_error_ensure(indices != NULL, cpl_error_get_code(),
goto cleanup,
2816 "Could not fetch the '%s' column from the fiber setup"
2817 " table in '%s'.", GIALIAS_COLUMN_INDEX, infilename);
2818 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2819 cpl_size oldindex = indices[i];
2820 cpl_size newindex = i+1;
2821 indices[i] = newindex;
2822 subimg = cpl_image_extract(srcimg, oldindex, 1, oldindex, ny);
2823 cpl_error_ensure(subimg != NULL, cpl_error_get_code(),
goto cleanup,
2824 "Could not extract sub image from '%s' at column %"
2825 CPL_SIZE_FORMAT
".", infilename, oldindex);
2826 error |= cpl_image_copy(img, subimg, newindex, 1);
2827 cpl_image_delete(subimg);
2829 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2830 "Could write sub image from '%s' at column %"
2831 CPL_SIZE_FORMAT
" to new image in '%s' at column %"
2832 CPL_SIZE_FORMAT
".", infilename, oldindex, outputfile,
2838 cpl_error_ensure(retcode == 0, cpl_error_get_code(),
goto cleanup,
2839 "Failed to write image to file '%s'.", outputfile);
2841 cpl_error_ensure(retcode == 0, cpl_error_get_code(),
goto cleanup,
2842 "Failed to attach the fiber setup table to file '%s'.",
2848 error |= cpl_frameset_insert(allframes, frame);
2849 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2850 "Could not add a new frame to the frame list for '%s'.",
2855 return CPL_ERROR_NONE;
2859 cpl_image_delete(subimg);
2862 cpl_frame_delete(frame);
2863 cpl_propertylist_delete(comments);
2864 return cpl_error_get_code();
2874static char* _giraffe_calc_format_string(cpl_size maxfiles)
2876 double ndigits = 1.0;
2880 ndigits = ceil(log10((
double)maxfiles + 1.0));
2882 return cpl_sprintf(
"science_spectrum_%%0%.0f"CPL_SIZE_FORMAT
".fits",
2903static cxint _giraffe_make_sdp_spectra(
const cxchar* flux_filename,
2904 const cxchar* err_filename,
2906 cpl_frameset* allframes,
2907 const cpl_parameterlist* parlist,
2908 const cxchar* recipe_id)
2910 cxint result_code = 1;
2912 cpl_error_code error = CPL_ERROR_NONE;
2913 cpl_errorstate prestate;
2914 const char* ancillary_filename =
"science_ancillary.fits";
2917 GiTable* fibertable = NULL;
2918 const cxchar* fibertable_name = NULL;
2919 irplib_sdp_spectrum* spectrum = NULL;
2920 cpl_propertylist* extrakeys = cpl_propertylist_new();
2921 cpl_propertylist* tablekeys = cpl_propertylist_new();
2922 cpl_propertylist* props;
2923 char* pipe_id = cpl_sprintf(
"%s/%s", PACKAGE, VERSION);
2924 const char* dict_id = PRODUCT_DID;
2925 const cpl_frame* inherit = NULL;
2926 cpl_frameset* usedframes = NULL;
2927 cpl_frameset* rawframes = NULL;
2928 cpl_frameset_iterator* iterator = NULL;
2929 cpl_size nx, ny, i, filecount;
2930 double exptime = NAN;
2931 double mjdobs = NAN;
2932 double mjdend = NAN;
2933 double wavelmin = NAN;
2934 double wavelmax = NAN;
2935 double specbin = NAN;
2936 double crpix2 = NAN;
2937 double crval2 = NAN;
2938 double cdelt2 = NAN;
2939 const char* cunit2 = NULL;
2941 const char* expmode = NULL;
2943 const int* indices = NULL;
2944 const int* fps = NULL;
2945 const char** objects = NULL;
2946 const char** spectypes = NULL;
2947 const double* ras = NULL;
2948 const double* decs = NULL;
2949 const double* gcorr = NULL;
2950 const double* hcorr = NULL;
2951 const double* bcorr = NULL;
2952 char* formatstr = NULL;
2953 char* filename = NULL;
2954 cpl_type wavecoltype;
2955 cpl_array* refwavearray = NULL;
2956 cpl_array* array = NULL;
2957 float* data_float = NULL;
2958 double* data_double = NULL;
2959 cpl_vector* fluximgcol = NULL;
2960 cpl_vector* errimgcol = NULL;
2961 cpl_boolean got_ancillary_data = CPL_FALSE;
2962 cpl_size assoc_key_offset = 1;
2964 double lamrms = NAN;
2965 double specerr = NAN;
2966 double specsye = NAN;
2968 const char *dateobs = NULL;
2970 cpl_error_ensure(flux_filename != NULL && err_filename != NULL
2971 && allframes != NULL && parlist != NULL
2972 && recipe_id != NULL, CPL_ERROR_NULL_INPUT,
goto cleanup,
2973 "NULL input parameters.");
2975 error |= cpl_propertylist_append_string(extrakeys, GIALIAS_PROCATG,
2976 GIALIAS_PROCATG_RBNSPEC_IDP);
2977 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_PROCATG,
2978 GIALIAS_PROCATG_COMMENT);
2979 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
2980 "Could not set keyword '%s'.", GIALIAS_PROCATG);
2984 cpl_error_ensure(errorcode == 0, cpl_error_get_code(),
goto cleanup,
2985 "Could not load image data in primary HDU from '%s'.",
2988 cpl_error_ensure(errorcode == 0, cpl_error_get_code(),
goto cleanup,
2989 "Could not load image data in primary HDU from '%s'.",
2992 giraffe_error_push();
2994 if (fibertable == NULL) {
2996 GIALIAS_FIBER_SETUP);
2997 fibertable_name = err_filename;
2999 fibertable_name = flux_filename;
3001 cpl_error_ensure(fibertable != NULL, CPL_ERROR_DATA_NOT_FOUND,
goto cleanup,
3002 "Could not load the %s table from either '%s' or '%s'.",
3003 GIALIAS_FIBER_SETUP, flux_filename, err_filename);
3004 giraffe_error_pop();
3011 CPL_ERROR_INCOMPATIBLE_INPUT,
goto cleanup,
3012 "The images in files '%s' and '%s' are not the same size.",
3013 flux_filename, err_filename);
3017 usedframes = cpl_frameset_new();
3018 rawframes = cpl_frameset_new();
3019 iterator = cpl_frameset_iterator_new(allframes);
3021 const cpl_frame* frame = cpl_frameset_iterator_get_const(iterator);
3022 if (frame != NULL) {
3023 switch (cpl_frame_get_group(frame)) {
3024 case CPL_FRAME_GROUP_RAW:
3026 if (inherit == NULL) inherit = frame;
3027 error |= cpl_frameset_insert(rawframes,
3028 cpl_frame_duplicate(frame));
3029 error |= cpl_frameset_insert(usedframes,
3030 cpl_frame_duplicate(frame));
3032 case CPL_FRAME_GROUP_CALIB:
3033 error |= cpl_frameset_insert(usedframes,
3034 cpl_frame_duplicate(frame));
3040 prestate = cpl_errorstate_get();
3041 error |= cpl_frameset_iterator_advance(iterator, 1);
3042 if (error == CPL_ERROR_ACCESS_OUT_OF_RANGE) {
3043 cpl_errorstate_set(prestate);
3045 }
else if (error != CPL_ERROR_NONE) {
3050 cpl_error_ensure(inherit != NULL, CPL_ERROR_DATA_NOT_FOUND,
goto cleanup,
3051 "No raw input frames found.");
3055 prestate = cpl_errorstate_get();
3056 exptime = cpl_propertylist_get_double(props, GIALIAS_EXPTIME);
3057 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3058 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3059 GIALIAS_EXPTIME, flux_filename);
3060 mjdobs = cpl_propertylist_get_double(props, GIALIAS_MJDOBS);
3061 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3062 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3063 GIALIAS_MJDOBS, flux_filename);
3065 mjdend = mjdobs + exptime / 86400.;
3069 dateobs = cpl_propertylist_get_string(props, GIALIAS_DATEOBS);
3070 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3071 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3072 GIALIAS_DATEOBS, flux_filename);
3074 obsid = cpl_propertylist_get_int(props, GIALIAS_OBSID);
3075 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3076 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3077 GIALIAS_OBSID, flux_filename);
3081 crpix2 = cpl_propertylist_get_double(props, GIALIAS_CRPIX2);
3082 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3083 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3084 GIALIAS_CRPIX2, flux_filename);
3085 crval2 = cpl_propertylist_get_double(props, GIALIAS_CRVAL2);
3086 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3087 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3088 GIALIAS_CRVAL2, flux_filename);
3089 cdelt2 = cpl_propertylist_get_double(props, GIALIAS_CDELT2);
3090 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3091 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3092 GIALIAS_CDELT2, flux_filename);
3093 cunit2 = cpl_propertylist_get_string(props, GIALIAS_CUNIT2);
3094 cpl_error_ensure(cunit2 != NULL, cpl_error_get_code(),
3095 goto cleanup,
"Could not find keyword '%s' in '%s'.",
3096 GIALIAS_CUNIT2, flux_filename);
3098 if (strcmp(cunit2,
"nm") == 0) {
3099 wavelmin = (1.0 - crpix2) * cdelt2 + crval2;
3100 wavelmax = ((double)ny - crpix2) * cdelt2 + crval2;
3101 if (wavelmax < wavelmin) {
3102 double tmp = wavelmin;
3103 wavelmin = wavelmax;
3106 specbin = fabs(cdelt2);
3108 cpl_msg_warning(cpl_func,
"Do not know how to handle keyword %s = '%s'."
3109 " Will not set WAVELMIN, WAVELMAX or SPEC_BIN.",
3110 GIALIAS_CUNIT2, cunit2);
3113 if (cpl_propertylist_has(props, GIALIAS_SETUPNAME)) {
3114 expmode = cpl_propertylist_get_string(props, GIALIAS_SETUPNAME);
3115 cpl_error_ensure(expmode != NULL, cpl_error_get_code(),
goto cleanup,
3116 "Could not fetch the keyword '%s' from '%s'.",
3117 GIALIAS_SETUPNAME, flux_filename);
3118 }
else if (cpl_propertylist_has(props, GIALIAS_GRATNAME)) {
3119 const char* name = cpl_propertylist_get_string(props, GIALIAS_GRATNAME);
3120 cpl_error_ensure(name != NULL, cpl_error_get_code(),
goto cleanup,
3121 "Could not fetch the keyword '%s' from '%s'.",
3122 GIALIAS_GRATNAME, flux_filename);
3123 double wlen = cpl_propertylist_get_double(props, GIALIAS_GRATWLEN);
3124 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3125 cpl_error_get_code(),
goto cleanup,
3126 "Could not find keyword '%s' in '%s'.",
3127 GIALIAS_GRATWLEN, flux_filename);
3128 strbuf[0] = name[0];
3129 char* numstr = cpl_sprintf(
"%.1f", wlen);
3130 strncpy(strbuf+1, numstr,
sizeof(strbuf)-1);
3132 strbuf[
sizeof(strbuf)-1] =
'\0';
3135 cpl_error_set_message(cpl_func, CPL_ERROR_DATA_NOT_FOUND,
3136 "Neither '%s' nor '%s' and '%s' keywords were found in the"
3137 " file '%s'.", GIALIAS_SETUPNAME, GIALIAS_GRATNAME,
3138 GIALIAS_GRATWLEN, flux_filename);
3142 specres = _giraffe_lookup_specres(expmode);
3143 if (isnan(specres)) {
3144 cpl_error_set_message(cpl_func, CPL_ERROR_ILLEGAL_INPUT,
3145 "The exposure mode '%s' is invalid or an unknown value."
3146 " Could not lookup the spectral resolution for 'SPEC_RES'.",
3153 if (cpl_propertylist_has(props,
"FILTER")) {
3154 prestate = cpl_errorstate_get();
3155 cpl_propertylist_copy_property(extrakeys, props,
"FILTER");
3156 cpl_property* prop = cpl_propertylist_get_property(extrakeys,
"FILTER");
3157 cpl_property_set_name(prop,
"OFILTER");
3158 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3159 cpl_error_get_code(),
goto cleanup,
3160 "Could not rename the 'FILTER' keyword.");
3164 prestate = cpl_errorstate_get();
3165 got_ancillary_data = _giraffe_ancillary_data_available(flux_filename,
3167 if (! cpl_errorstate_is_equal(prestate))
goto cleanup;
3168 if (got_ancillary_data) {
3169 error = _giraffe_make_ancillary_file(allframes, ancillary_filename,
3170 flux_filename, fluximage,
3172 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3173 "Failed to write the ancillary file '%s'.",
3174 ancillary_filename);
3178 spectrum = irplib_sdp_spectrum_new();
3179 error = CPL_ERROR_NONE;
3180 error |= irplib_sdp_spectrum_set_origin(spectrum, GIALIAS_ORIGIN_VALUE);
3181 error |= irplib_sdp_spectrum_set_prodlvl(spectrum, GIALIAS_PRODLVL_VALUE);
3182 error |= irplib_sdp_spectrum_copy_dispelem(spectrum,
3183 props, GIALIAS_GRATNAME);
3184 error |= irplib_sdp_spectrum_set_specsys(spectrum, GIALIAS_SPECSYS_VALUE);
3185 error |= irplib_sdp_spectrum_set_extobj(spectrum, GIALIAS_EXT_OBJ_VALUE);
3188 error |= irplib_sdp_spectrum_set_object(spectrum,
"");
3189 error |= irplib_sdp_spectrum_set_ra(spectrum, 0.0);
3190 error |= irplib_sdp_spectrum_set_dec(spectrum, 0.0);
3191 error |= irplib_sdp_spectrum_copy_exptime(spectrum, props, GIALIAS_EXPTIME);
3192 error |= irplib_sdp_spectrum_copy_texptime(spectrum,
3193 props, GIALIAS_EXPTIME);
3194 error |= irplib_sdp_spectrum_copy_mjdobs(spectrum, props, GIALIAS_MJDOBS);
3195 error |= irplib_sdp_spectrum_set_mjdend(spectrum, mjdend);
3196 if (cpl_propertylist_has(props, GIALIAS_TIMESYS)) {
3197 error |= irplib_sdp_spectrum_copy_timesys(spectrum,
3198 props, GIALIAS_TIMESYS);
3200 error |= irplib_sdp_spectrum_copy_progid(spectrum, props, GIALIAS_PROGID);
3201 error |= irplib_sdp_spectrum_copy_obid(spectrum, 1, props, GIALIAS_OBSID);
3202 error |= irplib_sdp_spectrum_set_mepoch(spectrum, GIALIAS_M_EPOCH_VALUE);
3203 error |= irplib_sdp_spectrum_append_prov(spectrum, 1, rawframes);
3204 error |= irplib_sdp_spectrum_copy_procsoft(spectrum,
3205 props, GIALIAS_PROPIPEID);
3206 error |= irplib_sdp_spectrum_copy_obstech(spectrum, props, GIALIAS_PROTECH);
3207 error |= irplib_sdp_spectrum_set_prodcatg(spectrum, GIALIAS_PRODCATG_VALUE);
3208 error |= irplib_sdp_spectrum_set_fluxcal(spectrum, GIALIAS_FLUXCAL_VALUE);
3209 error |= irplib_sdp_spectrum_set_contnorm(spectrum, GIALIAS_CONTNORM_VALUE);
3213 error |= irplib_sdp_spectrum_set_wavelmin(spectrum, 0.0);
3214 error |= irplib_sdp_spectrum_set_wavelmax(spectrum, 0.0);
3215 error |= irplib_sdp_spectrum_set_specbin(spectrum, 0.0);
3216 error |= irplib_sdp_spectrum_set_totflux(spectrum, GIALIAS_TOTFLUX_VALUE);
3217 error |= irplib_sdp_spectrum_set_fluxerr(spectrum, GIALIAS_FLUXERR_VALUE);
3218 error |= irplib_sdp_spectrum_set_ncombine(spectrum,
3219 cpl_frameset_get_size(rawframes));
3220 error |= irplib_sdp_spectrum_set_referenc(spectrum, GIALIAS_REFERENC);
3223 error |= irplib_sdp_spectrum_set_snr(spectrum, 0.0);
3226 if (cpl_propertylist_has(props, GIALIAS_LAMNLIN)) {
3227 error |= irplib_sdp_spectrum_copy_lamnlin(spectrum, props,
3229 lamnlin = irplib_sdp_spectrum_get_lamnlin(spectrum);
3231 lamnlin = _giraffe_lookup_lamnlin(expmode);
3232 if (lamnlin != -1) {
3233 error |= irplib_sdp_spectrum_set_lamnlin(spectrum, lamnlin);
3240 if (cpl_propertylist_has(props, GIALIAS_LAMRMS)) {
3241 error |= irplib_sdp_spectrum_copy_lamrms(spectrum, props,
3243 lamrms = irplib_sdp_spectrum_get_lamrms(spectrum);
3245 lamrms = _giraffe_lookup_lamrms(expmode);
3246 if (! isnan(lamrms)) {
3247 error |= irplib_sdp_spectrum_set_lamrms(spectrum, lamrms);
3261 if (cpl_propertylist_has(props, GIALIAS_SPEC_ERR)) {
3262 error |= irplib_sdp_spectrum_copy_specerr(spectrum, props,
3264 specerr = irplib_sdp_spectrum_get_specerr(spectrum);
3265 }
else if (lamnlin > 0) {
3266 if (cpl_propertylist_has(props, GIALIAS_CRDER1)) {
3267 prestate = cpl_errorstate_get();
3268 double crder1 = cpl_propertylist_get_double(props, GIALIAS_CRDER1);
3269 if (cpl_errorstate_is_equal(prestate) && crder1 > 0) {
3270 specerr = crder1 / sqrt(lamnlin);
3272 error = cpl_error_get_code();
3274 }
else if (! isnan(lamrms)) {
3275 specerr = lamrms / sqrt(lamnlin);
3277 if (! isnan(specerr)) {
3278 error |= irplib_sdp_spectrum_set_specerr(spectrum, specerr);
3285 if (cpl_propertylist_has(props, GIALIAS_SPEC_SYE)) {
3286 error |= irplib_sdp_spectrum_copy_specsye(spectrum, props,
3288 specsye = irplib_sdp_spectrum_get_specsye(spectrum);
3293 error |= irplib_sdp_spectrum_set_specsye(spectrum, 0.002);
3296 error |= irplib_sdp_spectrum_set_specres(spectrum, specres);
3297 error |= irplib_sdp_spectrum_copy_gain(spectrum, props, GIALIAS_CONAD);
3298 error |= irplib_sdp_spectrum_copy_detron(spectrum, props, GIALIAS_RON);
3299 if (got_ancillary_data) {
3300 error |= irplib_sdp_spectrum_set_asson(spectrum, 1, ancillary_filename);
3301 error |= irplib_sdp_spectrum_set_assoc(spectrum, 1,
3302 GIALIAS_ASSOC_VALUE);
3303 error |= irplib_sdp_spectrum_set_assom(spectrum, 1,
"");
3304 assoc_key_offset = 2;
3306 for (i = assoc_key_offset; i < nassoc_keys + assoc_key_offset; ++i) {
3308 error |= irplib_sdp_spectrum_set_asson(spectrum, i,
"");
3309 error |= irplib_sdp_spectrum_set_assoc(spectrum, i,
"");
3310 error |= irplib_sdp_spectrum_set_assom(spectrum, i,
"");
3313 error |= irplib_sdp_spectrum_set_voclass(spectrum, GIALIAS_VOCLASS_VALUE);
3314 error |= irplib_sdp_spectrum_set_vopub(spectrum, GIALIAS_VOPUB_VALUE);
3315 error |= irplib_sdp_spectrum_set_title(spectrum,
"");
3316 error |= cpl_propertylist_append_double(tablekeys, GIALIAS_APERTURE,
3317 GIALIAS_APERTURE_VALUE);
3318 error |= cpl_propertylist_set_comment(tablekeys, GIALIAS_APERTURE,
3319 GIALIAS_APERTURE_COMMENT);
3328 error |= irplib_sdp_spectrum_set_telapse(spectrum, exptime);
3329 error |= irplib_sdp_spectrum_set_tmid(spectrum, (mjdobs + mjdend) * 0.5);
3333 error |= irplib_sdp_spectrum_set_specval(spectrum, 0.0);
3334 error |= irplib_sdp_spectrum_set_specbw(spectrum, 0.0);
3335 error |= irplib_sdp_spectrum_set_nelem(spectrum, ny);
3336 error |= irplib_sdp_spectrum_set_tdmin(spectrum, 0.0);
3337 error |= irplib_sdp_spectrum_set_tdmax(spectrum, 0.0);
3340 error |= cpl_propertylist_append_int(extrakeys, GIALIAS_FPS, -1);
3341 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_FPS,
3342 GIALIAS_FPS_COMMENT);
3345 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_GEOCORR, NAN);
3346 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_GEOCORR,
3347 GIALIAS_GEOCORR_COMMENT);
3348 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_HELICORR, NAN);
3349 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_HELICORR,
3350 GIALIAS_HELICORR_COMMENT);
3351 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_BARYCORR, NAN);
3352 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_BARYCORR,
3353 GIALIAS_BARYCORR_COMMENT);
3355 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3356 "Could not setup the common SDP spectrum keywords.");
3358 for (
int qci = 0; qci <
sizeof(sciqcpar) /
sizeof(sciqcpar[0]); qci++) {
3359 if (cpl_propertylist_has(props, sciqcpar[qci])) {
3360 cpl_propertylist_copy_property(extrakeys, props, sciqcpar[qci]);
3366 wavecoltype = _giraffe_calc_wave_type(crval2, crpix2, cdelt2, ny);
3369 refwavearray = cpl_array_new(ny, CPL_TYPE_DOUBLE);
3370 data_double = cpl_array_get_data_double(refwavearray);
3371 assert(data_double != NULL);
3372 for (i = 1; i <= ny; ++i) {
3373 data_double[i-1] = (i-crpix2) * cdelt2 + crval2;
3378 error |= irplib_sdp_spectrum_add_column(
3379 spectrum, GIALIAS_COLUMN_WAVE, wavecoltype,
3380 GIALIAS_COLUMN_WAVE_UNIT, NULL, GIALIAS_COLUMN_WAVE_TUTYP,
3381 GIALIAS_COLUMN_WAVE_TUCD, NULL);
3384 error |= irplib_sdp_spectrum_replace_column_comment(
3385 spectrum, GIALIAS_COLUMN_WAVE,
"TUCD",
"Air wavelength");
3387 error |= irplib_sdp_spectrum_set_column_tcomm(
3388 spectrum, GIALIAS_COLUMN_WAVE, GIALIAS_COLUMN_WAVE_TCOMM);
3389 error |= irplib_sdp_spectrum_add_column(
3390 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, CPL_TYPE_DOUBLE,
3391 GIALIAS_COLUMN_FLUX_REDUCED_UNIT, NULL,
3392 GIALIAS_COLUMN_FLUX_REDUCED_TUTYP,
3393 GIALIAS_COLUMN_FLUX_REDUCED_TUCD, NULL);
3394 error |= irplib_sdp_spectrum_set_column_tcomm(
3395 spectrum, GIALIAS_COLUMN_FLUX_REDUCED,
"");
3396 error |= irplib_sdp_spectrum_add_column(
3397 spectrum, GIALIAS_COLUMN_ERR_REDUCED, CPL_TYPE_DOUBLE,
3398 GIALIAS_COLUMN_ERR_REDUCED_UNIT, NULL,
3399 GIALIAS_COLUMN_ERR_REDUCED_TUTYP,
3400 GIALIAS_COLUMN_ERR_REDUCED_TUCD, NULL);
3401 error |= irplib_sdp_spectrum_set_column_tcomm(
3402 spectrum, GIALIAS_COLUMN_ERR_REDUCED,
"");
3403 error |= irplib_sdp_spectrum_add_column(
3404 spectrum, GIALIAS_COLUMN_SNR, CPL_TYPE_DOUBLE,
3405 GIALIAS_COLUMN_SNR_UNIT, NULL, GIALIAS_COLUMN_SNR_TUTYP,
3406 GIALIAS_COLUMN_SNR_TUCD, NULL);
3407 error |= irplib_sdp_spectrum_set_column_tcomm(
3408 spectrum, GIALIAS_COLUMN_SNR, GIALIAS_COLUMN_SNR_TCOMM);
3409 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3410 "Could not setup the SDP spectrum columns.");
3413 GIALIAS_COLUMN_INDEX);
3417 GIALIAS_COLUMN_OBJECT);
3419 GIALIAS_COLUMN_TYPE);
3423 GIALIAS_COLUMN_DEC);
3425 GIALIAS_COLUMN_GCORR);
3427 GIALIAS_COLUMN_HCORR);
3429 GIALIAS_COLUMN_BCORR);
3430 cpl_error_ensure(indices != NULL && fps != NULL && objects != NULL
3431 && spectypes != NULL && ras != NULL && decs != NULL
3432 && gcorr != NULL && hcorr != NULL && bcorr != NULL,
3433 cpl_error_get_code(),
goto cleanup,
3434 "Could not fetch data from the fiber setup table in '%s'.",
3437 formatstr = _giraffe_calc_format_string(
3440 cpl_errorstate tempes = cpl_errorstate_get();
3445 cpl_image_get_maxpos(maxim, &maxx, &maxy);
3447 cpl_image_delete(maxim);
3449 cpl_errorstate_set(tempes);
3454 const double* wave_data;
3460 const char* remregexp =
"^(CDELT[0-9]+|CD[0-9]+_[0-9]+|CRPIX[0-9]+"
3461 "|CRDER[0-9]+|CSYER[0-9]+|BUNIT|BSCALE|BZERO"
3463 cpl_size specindex = indices[i];
3464 double vela, velb, beta;
3465 double correction_factor = 1.0;
3468 if (strcmp(spectypes[i],
"M") != 0)
continue;
3470 filename = cpl_sprintf(formatstr, ++filecount);
3475 vela = gcorr[i] * 1e3;
3476 velb = hcorr[i] * 1e3;
3477 beta = (vela + velb) / CPL_PHYS_C;
3478 cpl_error_ensure(-1 <= beta && beta <= 1,
3479 CPL_ERROR_ILLEGAL_OUTPUT,
goto cleanup,
3480 "The velocities GCORR = %g and HCORR = %g for spectrum"
3481 "%"CPL_SIZE_FORMAT
" in file '%s' give invalid"
3482 " Heliocentric correction factor values.",
3483 gcorr[i], hcorr[i], specindex, flux_filename);
3484 correction_factor = sqrt((1.0 + beta) / (1.0 - beta));
3488 wave_data = cpl_array_get_data_double_const(refwavearray);
3489 if (wavecoltype == CPL_TYPE_FLOAT) {
3490 data_float = cpl_malloc(ny *
sizeof(
float));
3491 for (j = 0; j < ny; ++j) {
3492 data_float[j] = wave_data[j] * correction_factor;
3494 array = cpl_array_wrap_float(data_float, ny);
3496 data_double = cpl_malloc(ny *
sizeof(
double));
3497 for (j = 0; j < ny; ++j) {
3498 data_double[j] = wave_data[j] * correction_factor;
3500 array = cpl_array_wrap_double(data_double, ny);
3502 error |= irplib_sdp_spectrum_set_column_data(
3503 spectrum, GIALIAS_COLUMN_WAVE, array);
3504 cpl_array_unwrap(array);
3507 fluximgcol = cpl_vector_new_from_image_column(
3509 flux_data = cpl_vector_get_data(fluximgcol);
3510 cpl_error_ensure(flux_data != NULL, cpl_error_get_code(),
goto cleanup,
3511 "Unable to extract data in column %"CPL_SIZE_FORMAT
3512 " from image in file '%s'.", specindex, flux_filename);
3513 array = cpl_array_wrap_double(flux_data, ny);
3516 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG,
'Y');
3519 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG,
'N');
3522 double fluxmean = cpl_array_get_mean(array);
3523 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMEANRED, fluxmean);
3524 error |= irplib_sdp_spectrum_set_column_data(
3525 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, array);
3526 cpl_array_unwrap(array);
3529 errimgcol = cpl_vector_new_from_image_column(
3531 err_data = cpl_vector_get_data(errimgcol);
3532 cpl_error_ensure(err_data != NULL, cpl_error_get_code(),
goto cleanup,
3533 "Unable to extract data in column %"CPL_SIZE_FORMAT
3534 " from image in file '%s'.", specindex, err_filename);
3535 array = cpl_array_wrap_double(err_data, ny);
3536 error |= irplib_sdp_spectrum_set_column_data(
3537 spectrum, GIALIAS_COLUMN_ERR_REDUCED, array);
3538 cpl_array_unwrap(array);
3541 data_double = cpl_malloc(ny *
sizeof(
double));
3542 for (j = 0; j < ny; ++j) {
3543 data_double[j] = (err_data[j] != 0.0) ? flux_data[j] / err_data[j]
3546 array = cpl_array_wrap_double(data_double, ny);
3547 snr = cpl_array_get_median(array);
3548 double snrmean = cpl_array_get_mean(array);
3549 cpl_propertylist_update_double(extrakeys, GIALIAS_QCSNR, snrmean);
3550 error |= irplib_sdp_spectrum_set_column_data(spectrum,
3551 GIALIAS_COLUMN_SNR, array);
3552 cpl_array_unwrap(array);
3554 cpl_free(data_double);
3557 cpl_vector_delete(fluximgcol);
3559 cpl_vector_delete(errimgcol);
3564 estmag = cpl_table_get_double(
giraffe_table_get(fibertable),
"MAGNITUDE", i, NULL);
3566 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMAG, estmag);
3568 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3569 "Could not setup the SDP spectrum columns for '%s'.",
3572 error |= irplib_sdp_spectrum_set_object(spectrum, objects[i]);
3576 tmp_string = cpl_sprintf(
"%s_%d_%s",
3582 replace_spaces_with_underscores(tmp_string);
3584 error |= irplib_sdp_spectrum_set_title(spectrum, tmp_string);
3586 cpl_free(tmp_string);
3588 error |= irplib_sdp_spectrum_set_ra(spectrum, ras[i]);
3589 error |= irplib_sdp_spectrum_set_dec(spectrum, decs[i]);
3590 error |= irplib_sdp_spectrum_set_snr(spectrum, snr);
3591 error |= irplib_sdp_spectrum_set_column_tcomm(
3592 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, flux_filename);
3593 error |= irplib_sdp_spectrum_set_column_tcomm(
3594 spectrum, GIALIAS_COLUMN_ERR_REDUCED, err_filename);
3596 error |= cpl_propertylist_update_int(extrakeys, GIALIAS_FPS, fps[i]);
3597 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_GEOCORR,
3599 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_HELICORR,
3601 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_BARYCORR,
3605 error |= irplib_sdp_spectrum_set_wavelmin(spectrum,
3606 wavelmin * correction_factor);
3607 error |= irplib_sdp_spectrum_set_wavelmax(spectrum,
3608 wavelmax * correction_factor);
3609 error |= irplib_sdp_spectrum_set_specval(spectrum,
3610 (wavelmax + wavelmin) * 0.5 * correction_factor);
3611 error |= irplib_sdp_spectrum_set_specbw(spectrum,
3612 (wavelmax - wavelmin) * correction_factor);
3613 error |= irplib_sdp_spectrum_set_tdmin(spectrum,
3614 wavelmin * correction_factor);
3615 error |= irplib_sdp_spectrum_set_tdmax(spectrum,
3616 wavelmax * correction_factor);
3617 error |= irplib_sdp_spectrum_set_specbin(spectrum,
3618 specbin * correction_factor);
3619 if (! isnan(lamrms)) {
3620 error |= irplib_sdp_spectrum_set_lamrms(spectrum,
3621 lamrms * correction_factor);
3623 if (! isnan(specerr)) {
3624 error |= irplib_sdp_spectrum_set_specerr(spectrum,
3625 specerr * correction_factor);
3627 if (! isnan(specsye)) {
3628 error |= irplib_sdp_spectrum_set_specsye(spectrum,
3629 specsye * correction_factor);
3632 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3633 "Could not setup the SDP spectrum keywords for '%s'.",
3636 error |= irplib_dfs_save_spectrum(allframes, NULL, parlist, usedframes,
3637 inherit, spectrum, recipe_id,
3638 extrakeys, tablekeys, remregexp,
3639 pipe_id, dict_id, filename);
3640 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3641 "Failed to save SDP spectrum %"CPL_SIZE_FORMAT
3642 " to file '%s'.", specindex, filename);
3644 error |= irplib_fits_update_checksums(filename);
3645 cpl_error_ensure(! error, cpl_error_get_code(),
goto cleanup,
3646 "Failed to save update checksums for file '%s'.",
3652 if (filecount == 0) {
3653 cpl_msg_warning(cpl_func,
"No science spectra found in '%s'."
3654 " No SDP spectra created.", flux_filename);
3662 cpl_vector_delete(fluximgcol);
3663 cpl_vector_delete(errimgcol);
3664 cpl_array_unwrap(array);
3665 cpl_array_delete(refwavearray);
3666 cpl_free(data_float);
3667 cpl_free(data_double);
3669 cpl_free(formatstr);
3670 cpl_frameset_delete(usedframes);
3671 cpl_frameset_delete(rawframes);
3672 cpl_frameset_iterator_delete(iterator);
3674 cpl_propertylist_delete(tablekeys);
3675 cpl_propertylist_delete(extrakeys);
3679 irplib_sdp_spectrum_delete(spectrum);
cxint giraffe_add_rvcorrection(GiTable *fibers, const GiImage *spectra)
Add the barycentric and heliocentric corrections to the given fiber setup.
GiBiasConfig * giraffe_bias_config_create(cpl_parameterlist *list)
Creates a setup structure for a bias removal task.
void giraffe_bias_config_add(cpl_parameterlist *list)
Adds parameters for the bias removal.
cxint giraffe_bias_remove(GiImage *result, const GiImage *raw, const GiImage *master_bias, const GiImage *bad_pixels, const cpl_matrix *biaslimits, const GiBiasConfig *config)
Removes the bias from an image.
void giraffe_bias_config_destroy(GiBiasConfig *config)
Destroys a bias removal setup structure.
cxint giraffe_subtract_dark(GiImage *image, const GiImage *dark, const GiImage *bpixel, GiDarkResults *data, const GiDarkConfig *config)
Subtract the dark current from a bias corrected image.
GiTable * giraffe_fibers_setup(const cpl_frame *frame, const cpl_frame *reference)
Setup a fiber list.
GiTable * giraffe_fiberlist_load(const cxchar *filename, cxint dataset, const cxchar *tag)
Load a fiber table from a file.
cxint giraffe_fiberlist_compare(const GiTable *fibers, const GiTable *reference)
Compare two fiber lists.
cxint giraffe_fiberlist_attach(cpl_frame *frame, GiTable *fibers)
Attach a fiber table to a frame.
GiFlatConfig * giraffe_flat_config_create(cpl_parameterlist *list)
Creates a setup structure for the flat field correction.
void giraffe_flat_config_destroy(GiFlatConfig *config)
Destroys a flat field setup structure.
void giraffe_flat_config_add(cpl_parameterlist *list)
Adds parameters for the flat field correction.
cxint giraffe_flat_apply(GiExtraction *extraction, const GiTable *fibers, const GiImage *flat, const GiImage *errors, GiFlatConfig *config)
Apply the flat field correction to the given extracted spectra.
GiFieldOfViewConfig * giraffe_fov_config_create(cpl_parameterlist *list)
Creates a setup structure for the field of view reconstruction.
void giraffe_fov_config_destroy(GiFieldOfViewConfig *config)
Destroys a field of view setup structure.
GiFieldOfView * giraffe_fov_new(void)
Create an empty container for the results of the field of view reconstruction.
cxint giraffe_fov_save_cubes_eso3d(const GiFieldOfView *self, cpl_propertylist *properties, const cxchar *filename, cxptr data)
Write the cube components of a field-of-view object to a file.
void giraffe_fov_delete(GiFieldOfView *self)
Deallocate a field of view object and its contents.
cxint giraffe_fov_build(GiFieldOfView *result, GiRebinning *rebinning, GiTable *fibers, GiTable *wsolution, GiTable *grating, GiTable *slitgeometry, GiFieldOfViewConfig *config)
Create and image and a data cube from extracted and rebinned spectra.
cxint giraffe_fov_save_cubes(const GiFieldOfView *self, cpl_propertylist *properties, const cxchar *filename, cxptr data)
Write the cube components of a field-of-view object to a file.
void giraffe_fov_config_add(cpl_parameterlist *list)
Adds parameters for the image and data cube construction.
cpl_frame * giraffe_frame_create(const cxchar *tag, cpl_frame_level level, const cpl_propertylist *properties, cxcptr object, cxcptr data, GiFrameCreator creator)
Create a product frame using a provided frame creator.
cpl_frame * giraffe_frame_create_image(GiImage *image, const cxchar *tag, cpl_frame_level level, cxbool save, cxbool update)
Create an image product frame.
cpl_frame * giraffe_get_slitgeometry(const cpl_frameset *set)
Get the slit geometry frame from a frame set.
cpl_image * giraffe_image_get(const GiImage *self)
Gets the image data.
cpl_propertylist * giraffe_image_get_properties(const GiImage *self)
Get the properties of an image.
void giraffe_image_delete(GiImage *self)
Destroys an image.
GiImage * giraffe_image_create(cpl_type type, cxint nx, cxint ny)
Creates an image container of a given type.
cxint giraffe_image_add_info(GiImage *image, const GiRecipeInfo *info, const cpl_frameset *set)
Add additional frame information to an image.
cxint giraffe_image_save(GiImage *self, const cxchar *filename)
Write a Giraffe image to a file.
GiImage * giraffe_image_new(cpl_type type)
Creates an empty image container.
cxint giraffe_image_set_properties(GiImage *self, cpl_propertylist *properties)
Attaches a property list to an image.
cxint giraffe_image_load(GiImage *self, const cxchar *filename, cxint position)
Gets image data and properties from a file.
void giraffe_rebin_config_destroy(GiRebinConfig *config)
Destroys a spectrum extraction setup structure.
cxint giraffe_rebin_spectra(GiRebinning *rebinning, const GiExtraction *extraction, const GiTable *fibers, const GiLocalization *localization, const GiTable *grating, const GiTable *slitgeo, const GiTable *solution, const GiRebinConfig *config)
Rebin an Extracted Spectra Frame and associated Errors Frame.
GiRebinConfig * giraffe_rebin_config_create(cpl_parameterlist *list)
Creates a setup structure for the rebinning.
GiRebinning * giraffe_rebinning_new(void)
Create an empty rebinning results container.
void giraffe_rebinning_destroy(GiRebinning *rebinning)
Destroys a rebinning results container and its contents.
void giraffe_rebin_config_add(cpl_parameterlist *list)
Adds parameters for the rebinning.
GiSGCalConfig * giraffe_sgcalibration_config_create(cpl_parameterlist *list)
Creates a setup structure for the slit geometry calibration.
cxint giraffe_compute_offsets(GiTable *fibers, const GiRebinning *rebinning, const GiTable *grating, const GiTable *mask, const GiSGCalConfig *config)
Compute wavelength offsets for a set of rebinned input spectrum.
void giraffe_sgcalibration_config_destroy(GiSGCalConfig *config)
Destroys a sgcalibration field setup structure.
void giraffe_sgcalibration_config_add(cpl_parameterlist *list)
Adds parameters for the sgcalibration correction computation.
GiTable * giraffe_slitgeometry_load(const GiTable *fibers, const cxchar *filename, cxint pos, const cxchar *tag)
Load the slit geometry information for a given fiber setup.
GiTable * giraffe_table_new(void)
Creates a new, empty Giraffe table.
GiTable * giraffe_table_duplicate(const GiTable *src)
Duplicate a Giraffe table.
cxint giraffe_table_load(GiTable *self, const cxchar *filename, cxint position, const cxchar *id)
Reads a data set from a file into a Giraffe table.
void giraffe_table_delete(GiTable *self)
Destroys a Giraffe table.
cpl_table * giraffe_table_get(const GiTable *self)
Get the table data from a Giraffe table.
cxint giraffe_add_frameset_info(cpl_propertylist *plist, const cpl_frameset *set, cxint sequence)
Add frameset specific information to a property list.
cxint giraffe_propertylist_copy(cpl_propertylist *self, const cxchar *name, const cpl_propertylist *other, const cxchar *othername)
Copy a property from one list to another.
const cxchar * giraffe_get_license(void)
Get the pipeline copyright and license.
GiInstrumentMode giraffe_get_mode(cpl_propertylist *properties)
Determines the instrument mode from a property list.
Slit geometry calibration configuration data structure.