GIRAFFE Pipeline Reference Manual
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GIRAFFE
Credits
giscience.c
1/*
2 * This file is part of the GIRAFFE Pipeline
3 * Copyright (C) 2002-2019 European Southern Observatory
4 *
5 * This program is free software; you can redistribute it and/or modify
6 * it under the terms of the GNU General Public License as published by
7 * the Free Software Foundation; either version 2 of the License, or
8 * (at your option) any later version.
9 *
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
14 *
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
18 */
19
20#ifdef HAVE_CONFIG_H
21# include <config.h>
22#endif
23
24#include <assert.h>
25
26#include <cxslist.h>
27#include <cxmessages.h>
28
29#include <cpl_recipe.h>
30#include <cpl_plugininfo.h>
31#include <cpl_parameterlist.h>
32#include <cpl_frameset.h>
33#include <cpl_msg.h>
34#include <cpl_errorstate.h>
35
36#include <irplib_sdp_spectrum.h>
37
38#include "gialias.h"
39#include "giimage.h"
40#include "giframe.h"
41#include "gifibers.h"
42#include "gifiberutils.h"
43#include "gislitgeometry.h"
44#include "gipsfdata.h"
45#include "gibias.h"
46#include "gidark.h"
47#include "giextract.h"
48#include "giflat.h"
49#include "gitransmission.h"
50#include "girebinning.h"
51#include "gisgcalibration.h"
52#include "giastrometry.h"
53#include "gifov.h"
54#include "gimessages.h"
55#include "gierror.h"
56#include "giutils.h"
57
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,
64 GIALIAS_QCBRIGHTFLG
65};
66
67static cxint giscience(cpl_parameterlist*, cpl_frameset*);
68
69static cxint _giraffe_make_sdp_spectra(const cxchar* flux_filename,
70 const cxchar* err_filename,
71 cxint nassoc_keys,
72 cpl_frameset* allframes,
73 const cpl_parameterlist* parlist,
74 const cxchar* recipe_id);
75
76const cxdouble saturation = 60000.;
77
78/*-----------------------------------------------------------------------------
79 Utility functions
80 -----------------------------------------------------------------------------*/
81
82 static void replace_spaces_with_underscores(char *str)
83 {
84
85 for (int i = 0; str[i] != '\0'; i++) {
86 if (str[i] == ' ') {
87 str[i] = '_'; // Replace space with an underscore
88 }
89 }
90 }
91
92/*
93 * Create the recipe instance, i.e. setup the parameter list for this
94 * recipe and make it available to the application using the interface.
95 */
96
97static cxint
98giscience_create(cpl_plugin* plugin)
99{
100
101 cpl_recipe* recipe = (cpl_recipe*)plugin;
102
103 cpl_parameter* p = NULL;
104
105
106 giraffe_error_init();
107
108
109 /*
110 * We have to provide the option we accept to the application. We
111 * need to setup our parameter list and hook it into the recipe
112 * interface.
113 */
114
115 recipe->parameters = cpl_parameterlist_new();
116 cx_assert(recipe->parameters != NULL);
117
118
119 /*
120 * Fill the parameter list.
121 */
122
123 /* Bias removal */
124
125 giraffe_bias_config_add(recipe->parameters);
126
127 /* Dark subtraction */
128
129 /* TBD */
130
131 /* Spectrum extraction */
132
133 giraffe_extract_config_add(recipe->parameters);
134
135 /* Flat fielding and relative fiber transmission correction */
136
137 giraffe_flat_config_add(recipe->parameters);
138
139 /* Spectrum rebinning */
140
141 giraffe_rebin_config_add(recipe->parameters);
142
143 /* Simultaneous wavelength calibration correction */
144
145 p = cpl_parameter_new_value("giraffe.siwc.apply",
146 CPL_TYPE_BOOL,
147 "Enable simultaneous wavelength calibration "
148 "correction.",
149 "giraffe.siwc",
150 TRUE);
151
152 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "siwc-apply");
153 cpl_parameterlist_append(recipe->parameters, p);
154
155 giraffe_sgcalibration_config_add(recipe->parameters);
156
157 /* Image reconstruction (IFU and Argus only) */
158
159 giraffe_fov_config_add(recipe->parameters);
160
161 /* Science Data Product format generation parameters: */
162
163 p = cpl_parameter_new_value("giraffe.sdp.format.generate",
164 CPL_TYPE_BOOL,
165 "TRUE if additional files should be generated"
166 " in Science Data Product (SDP) format.",
167 "giraffe.sdp",
168 FALSE);
169
170 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI, "generate-SDP-format");
171 cpl_parameterlist_append(recipe->parameters, p);
172
173 p = cpl_parameter_new_value("giraffe.sdp.nassoc.keys",
174 CPL_TYPE_INT,
175 "Sets the number of dummy (empty) ASSONi,"
176 " ASSOCi and ASSOMi keywords to create.",
177 "giraffe.sdp",
178 (int)0);
179
180 cpl_parameter_set_alias(p, CPL_PARAMETER_MODE_CLI,
181 "dummy-association-keys");
182 cpl_parameterlist_append(recipe->parameters, p);
183
184 return 0;
185
186}
187
188
189/*
190 * Execute the plugin instance given by the interface.
191 */
192
193static cxint
194giscience_exec(cpl_plugin* plugin)
195{
196 cxint result;
197 cpl_errorstate prev_state;
198
199 cpl_recipe* recipe = (cpl_recipe*)plugin;
200
201
202 cx_assert(recipe->parameters != NULL);
203 cx_assert(recipe->frames != NULL);
204
205 prev_state = cpl_errorstate_get();
206 result = giscience(recipe->parameters, recipe->frames);
207 if (result != 0) {
208 cpl_errorstate_dump(prev_state, CPL_FALSE, cpl_errorstate_dump_one);
209 }
210 return result;
211}
212
213
214static cxint
215giscience_destroy(cpl_plugin* plugin)
216{
217
218 cpl_recipe* recipe = (cpl_recipe*)plugin;
219
220
221 /*
222 * We just destroy what was created during the plugin initialization
223 * phase, i.e. the parameter list. The frame set is managed by the
224 * application which called us, so we must not touch it,
225 */
226
227 cpl_parameterlist_delete(recipe->parameters);
228
229 giraffe_error_clear();
230
231 return 0;
232
233}
234
235
236/*
237 * The actual recipe starts here.
238 */
239
240static cxint
241giscience(cpl_parameterlist* config, cpl_frameset* set)
242{
243
244 const cxchar* const _id = "giscience";
245
246
247 const cxchar* filename = NULL;
248
249 cxbool siwc = FALSE;
250 cxbool calsim = FALSE;
251
252 cxbool gensdp = FALSE;
253 cxint nassoc_keys = 0;
254 cxchar* flux_filename = NULL;
255 cxchar* err_filename = NULL;
256
257 cxint status = 0;
258
259 cxlong i;
260 cxlong nscience = 0;
261
262 cxdouble exptime = 0.;
263
264 cx_slist* slist = NULL;
265
266 cpl_propertylist* properties = NULL;
267
268 cpl_matrix* biasareas = NULL;
269
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;
285
286 cpl_parameter* p = NULL;
287
288 GiImage* mbias = NULL;
289 GiImage* mdark = NULL;
290 GiImage* bpixel = NULL;
291 GiImage* slight = NULL;
292 GiImage* sscience = NULL;
293 GiImage* rscience = NULL;
294
295 GiTable* fibers = NULL;
296 GiTable* slitgeometry = NULL;
297 GiTable* grating = NULL;
298 GiTable* wcalcoeff = NULL;
299
300 GiLocalization* localization = NULL;
301 GiExtraction* extraction = NULL;
302 GiRebinning* rebinning = NULL;
303
304 GiBiasConfig* bias_config = NULL;
305 GiExtractConfig* extract_config = NULL;
306 GiFlatConfig* flat_config = NULL;
307 GiRebinConfig* rebin_config = NULL;
308
309 GiInstrumentMode mode;
310
311 GiRecipeInfo info = {(cxchar*)_id, 1, NULL, config};
312
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}
332 };
333
334
335
336 if (!config) {
337 cpl_msg_error(_id, "Invalid parameter list! Aborting ...");
338 return 1;
339 }
340
341 if (!set) {
342 cpl_msg_error(_id, "Invalid frame set! Aborting ...");
343 return 1;
344 }
345
346 status = giraffe_frameset_set_groups(set, groups);
347
348 if (status != 0) {
349 cpl_msg_error(_id, "Setting frame group information failed!");
350 return 1;
351 }
352
353
354 /*
355 * Verify the frame set contents
356 */
357
358 nscience = cpl_frameset_count_tags(set, GIFRAME_SCIENCE);
359
360 if (nscience < 1) {
361 cpl_msg_error(_id, "Too few (%ld) raw frames (%s) present in "
362 "frame set! Aborting ...", nscience, GIFRAME_SCIENCE);
363 return 1;
364 }
365
366 locy_frame = cpl_frameset_find(set, GIFRAME_PSF_CENTROID);
367
368 if (locy_frame == NULL) {
369
370 locy_frame = cpl_frameset_find(set, GIFRAME_LOCALIZATION_CENTROID);
371
372 if (locy_frame == NULL) {
373 cpl_msg_info(_id, "No master localization (centroid position) "
374 "present in frame set. Aborting ...");
375 return 1;
376 }
377
378 }
379
380 locw_frame = cpl_frameset_find(set, GIFRAME_PSF_WIDTH);
381
382 if (locw_frame == NULL) {
383
384 locw_frame = cpl_frameset_find(set, GIFRAME_LOCALIZATION_WIDTH);
385
386 if (locw_frame == NULL) {
387 cpl_msg_info(_id, "No master localization (spectrum width) "
388 "present in frame set. Aborting ...");
389 return 1;
390 }
391
392 }
393
394 grating_frame = cpl_frameset_find(set, GIFRAME_GRATING);
395
396 if (!grating_frame) {
397 cpl_msg_error(_id, "No grating data present in frame set. "
398 "Aborting ...");
399 return 1;
400 }
401
402 slit_frame = giraffe_get_slitgeometry(set);
403
404 if (!slit_frame) {
405 cpl_msg_error(_id, "No slit geometry present in frame set. "
406 "Aborting ...");
407 return 1;
408 }
409
410 wcal_frame = cpl_frameset_find(set, GIFRAME_WAVELENGTH_SOLUTION);
411
412 if (!wcal_frame) {
413 cpl_msg_error(_id, "No dispersion solution present in frame set. "
414 "Aborting ...");
415 return 1;
416 }
417
418 linemask_frame = cpl_frameset_find(set, GIFRAME_LINE_MASK);
419
420 if (!linemask_frame) {
421 cpl_msg_warning(_id, "No reference line mask present in frame set.");
422 }
423
424 bpixel_frame = cpl_frameset_find(set, GIFRAME_BADPIXEL_MAP);
425
426 if (!bpixel_frame) {
427 cpl_msg_info(_id, "No bad pixel map present in frame set.");
428 }
429
430 mbias_frame = cpl_frameset_find(set, GIFRAME_BIAS_MASTER);
431
432 if (!mbias_frame) {
433 cpl_msg_info(_id, "No master bias present in frame set.");
434 }
435
436 mdark_frame = cpl_frameset_find(set, GIFRAME_DARK_MASTER);
437
438 if (!mdark_frame) {
439 cpl_msg_info(_id, "No master dark present in frame set.");
440 }
441
442 slight_frame = cpl_frameset_find(set, GIFRAME_SCATTERED_LIGHT_MODEL);
443
444 if (!slight_frame) {
445 cpl_msg_info(_id, "No scattered light model present in frame set.");
446 }
447
448 psfdata_frame = cpl_frameset_find(set, GIFRAME_PSF_DATA);
449
450 if (!psfdata_frame) {
451 cpl_msg_info(_id, "No PSF profile parameters present in frame set.");
452 }
453
454
455 /*
456 * Load raw images
457 */
458
459 slist = cx_slist_new();
460
461 science_frame = cpl_frameset_find(set, GIFRAME_SCIENCE);
462
463 for (i = 0; i < nscience; i++) {
464
465 filename = cpl_frame_get_filename(science_frame);
466
467 GiImage* raw = giraffe_image_new(CPL_TYPE_DOUBLE);
468
469
470 status = giraffe_image_load(raw, filename, 0);
471
472 if (status) {
473 cpl_msg_error(_id, "Cannot load raw science frame from '%s'. "
474 "Aborting ...", filename);
475
476 cx_slist_destroy(slist, (cx_free_func) giraffe_image_delete);
477
478 return 1;
479 }
480
481 cx_slist_push_back(slist, raw);
482
483 science_frame = cpl_frameset_find(set, NULL);
484
485 }
486
487 nscience = (cxint)cx_slist_size(slist);
488 sscience = cx_slist_pop_front(slist);
489
490 properties = giraffe_image_get_properties(sscience);
491 cx_assert(properties != NULL);
492
493 cpl_errorstate tempes = cpl_errorstate_get();
494 int nsaturated = -1;
495 cpl_image *sciim = giraffe_image_get(sscience);
496 if (sciim != NULL) {
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));
501 size_t scii;
502 nsaturated = 0;
503 for (scii = 0; scii < nxy; scii++) {
504 if (scipix[scii] > saturation)
505 nsaturated++;
506 }
507 }
508 }
509 cpl_errorstate_set(tempes);
510
511
512 cpl_propertylist_update_int(properties, GIALIAS_QCNSATSCI, nsaturated);
513
514 if (nscience > 1) {
515
516 /*
517 * Create a stacked science image from the list of raw images.
518 * Each raw image is disposed when it is no longer needed.
519 */
520
521 cpl_msg_info(_id, "Averaging science frames ...");
522
523 exptime = cpl_propertylist_get_double(properties, GIALIAS_EXPTIME);
524
525 for (i = 1; i < nscience; i++) {
526
527 cpl_propertylist* _properties;
528
529 GiImage* science = cx_slist_pop_front(slist);
530
531
532 cpl_image_add(giraffe_image_get(sscience),
533 giraffe_image_get(science));
534
535 _properties = giraffe_image_get_properties(science);
536 cx_assert(_properties != NULL);
537
538 exptime += cpl_propertylist_get_double(_properties, GIALIAS_EXPTIME);
539
540 giraffe_image_delete(science);
541
542 }
543
544 cpl_image_divide_scalar(giraffe_image_get(sscience), nscience);
545 }
546
547 cx_assert(cx_slist_empty(slist));
548 cx_slist_delete(slist);
549 slist = NULL;
550
551
552 if (nscience > 1) {
553
554 /*
555 * Update stacked science image properties
556 */
557
558 cpl_msg_info(_id, "Updating stacked science image properties ...");
559
560 cpl_propertylist_set_double(properties, GIALIAS_EXPTIME,
561 exptime / nscience);
562
563 cpl_propertylist_append_double(properties, GIALIAS_EXPTTOT, exptime);
564 cpl_propertylist_set_comment(properties, GIALIAS_EXPTTOT,
565 "Total exposure time of all frames "
566 "combined");
567
568 cpl_propertylist_erase(properties, GIALIAS_TPLEXPNO);
569
570 }
571
572 cpl_propertylist_append_int(properties, GIALIAS_DATANCOM, nscience);
573 cpl_propertylist_set_comment(properties, GIALIAS_DATANCOM,
574 "Number of combined frames");
575
576
577
578 /*
579 * Prepare for bias subtraction
580 */
581
582 bias_config = giraffe_bias_config_create(config);
583
584 /*
585 * Setup user defined areas to use for the bias computation
586 */
587
588 if (bias_config->method == GIBIAS_METHOD_MASTER ||
589 bias_config->method == GIBIAS_METHOD_ZMASTER) {
590
591 if (!mbias_frame) {
592 cpl_msg_error(_id, "Missing master bias frame! Selected bias "
593 "removal method requires a master bias frame!");
594
595 giraffe_bias_config_destroy(bias_config);
596 giraffe_image_delete(sscience);
597
598 return 1;
599 }
600 else {
601 filename = cpl_frame_get_filename(mbias_frame);
602
603
604 mbias = giraffe_image_new(CPL_TYPE_DOUBLE);
605 status = giraffe_image_load(mbias, filename, 0);
606
607 if (status) {
608 cpl_msg_error(_id, "Cannot load master bias from '%s'. "
609 "Aborting ...", filename);
610
611 giraffe_bias_config_destroy(bias_config);
612 giraffe_image_delete(sscience);
613
614 return 1;
615 }
616 }
617 }
618
619
620 /*
621 * Load bad pixel map if it is present in the frame set.
622 */
623
624 if (bpixel_frame) {
625
626 filename = cpl_frame_get_filename(bpixel_frame);
627
628
629 bpixel = giraffe_image_new(CPL_TYPE_INT);
630 status = giraffe_image_load(bpixel, filename, 0);
631
632 if (status) {
633 cpl_msg_error(_id, "Cannot load bad pixel map from '%s'. "
634 "Aborting ...", filename);
635
636 giraffe_image_delete(bpixel);
637 bpixel = NULL;
638
639 if (mbias != NULL) {
640 giraffe_image_delete(mbias);
641 mbias = NULL;
642 }
643
644 giraffe_bias_config_destroy(bias_config);
645 bias_config = NULL;
646
647 giraffe_image_delete(sscience);
648 sscience = NULL;
649
650 return 1;
651 }
652
653 }
654
655
656 /*
657 * Compute and remove the bias from the stacked flat field frame.
658 */
659
660 rscience = giraffe_image_new(CPL_TYPE_DOUBLE);
661
662 status = giraffe_bias_remove(rscience, sscience, mbias, bpixel, biasareas,
663 bias_config);
664
665 giraffe_image_delete(sscience);
666
667 if (mbias) {
668 giraffe_image_delete(mbias);
669 mbias = NULL;
670 }
671
672 giraffe_bias_config_destroy(bias_config);
673
674 if (status) {
675 cpl_msg_error(_id, "Bias removal failed. Aborting ...");
676
677 giraffe_image_delete(rscience);
678 rscience = NULL;
679
680 if (bpixel != NULL) {
681 giraffe_image_delete(bpixel);
682 bpixel = NULL;
683 }
684
685 return 1;
686 }
687
688
689 /*
690 * Load master dark if it is present in the frame set and correct
691 * the master flat field for the dark current.
692 */
693
694 if (mdark_frame) {
695
696 GiDarkConfig dark_config = {GIDARK_METHOD_ZMASTER, 0.};
697
698
699 cpl_msg_info(_id, "Correcting for dark current ...");
700
701 filename = cpl_frame_get_filename(mdark_frame);
702
703 mdark = giraffe_image_new(CPL_TYPE_DOUBLE);
704 status = giraffe_image_load(mdark, filename, 0);
705
706 if (status != 0) {
707 cpl_msg_error(_id, "Cannot load master dark from '%s'. "
708 "Aborting ...", filename);
709
710 giraffe_image_delete(rscience);
711 rscience = NULL;
712
713 if (bpixel != NULL) {
714 giraffe_image_delete(bpixel);
715 bpixel = NULL;
716 }
717
718 return 1;
719 }
720
721 status = giraffe_subtract_dark(rscience, mdark, bpixel, NULL,
722 &dark_config);
723
724 if (status != 0) {
725 cpl_msg_error(_id, "Dark subtraction failed! Aborting ...");
726
727 giraffe_image_delete(mdark);
728 mdark = NULL;
729
730 giraffe_image_delete(rscience);
731 rscience = NULL;
732
733 if (bpixel != NULL) {
734 giraffe_image_delete(bpixel);
735 bpixel = NULL;
736 }
737
738 return 1;
739 }
740
741 giraffe_image_delete(mdark);
742 mdark = NULL;
743
744 }
745
746
747 /*
748 * Update the reduced science properties, save the reduced science frame
749 * and register it as product.
750 */
751
752 cpl_msg_info(_id, "Writing pre-processed science image ...");
753
754 giraffe_image_add_info(rscience, &info, set);
755
756 rscience_frame = giraffe_frame_create_image(rscience,
757 GIFRAME_SCIENCE_REDUCED,
758 CPL_FRAME_LEVEL_INTERMEDIATE,
759 TRUE, TRUE);
760
761 if (rscience_frame == NULL) {
762 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
763
764 giraffe_image_delete(rscience);
765
766 return 1;
767 }
768
769 cpl_frameset_insert(set, rscience_frame);
770
771
772 /*
773 * Determine fiber setup
774 */
775
776 science_frame = cpl_frameset_find(set, GIFRAME_SCIENCE);
777
778 cpl_msg_info(_id, "Building fiber setup for frame '%s'.",
779 cpl_frame_get_filename(science_frame));
780
781 fibers = giraffe_fibers_setup(science_frame, locy_frame);
782
783 if (!fibers) {
784 cpl_msg_error(_id, "Cannot create fiber setup for frame '%s'! "
785 "Aborting ...", cpl_frame_get_filename(science_frame));
786
787 if (bpixel) {
788 giraffe_image_delete(bpixel);
789 bpixel = NULL;
790 }
791
792 giraffe_image_delete(rscience);
793 rscience = NULL;
794
795 return 1;
796 }
797
798 cpl_msg_info(_id, "Fiber reference setup taken from localization "
799 "frame '%s'.", cpl_frame_get_filename(locy_frame));
800
801
802 /*
803 * Load fiber localization
804 */
805
806 localization = giraffe_localization_new();
807
808 filename = cpl_frame_get_filename(locy_frame);
809
810 localization->locy = giraffe_image_new(CPL_TYPE_DOUBLE);
811 status = giraffe_image_load(localization->locy, filename, 0);
812
813 if (status) {
814 cpl_msg_error(_id, "Cannot load localization (centroid "
815 "position) frame from '%s'. Aborting ...",
816 filename);
817
818 giraffe_localization_destroy(localization);
819
820 if (bpixel) {
821 giraffe_image_delete(bpixel);
822 bpixel = NULL;
823 }
824
825 giraffe_table_delete(fibers);
826 giraffe_image_delete(rscience);
827
828 return 1;
829 }
830
831
832 filename = cpl_frame_get_filename(locw_frame);
833
834 localization->locw = giraffe_image_new(CPL_TYPE_DOUBLE);
835 status = giraffe_image_load(localization->locw, filename, 0);
836
837 if (status) {
838 cpl_msg_error(_id, "Cannot load localization (spectrum width) "
839 "frame from '%s'. Aborting ...", filename);
840
841 giraffe_localization_destroy(localization);
842
843 if (bpixel) {
844 giraffe_image_delete(bpixel);
845 bpixel = NULL;
846 }
847
848 giraffe_table_delete(fibers);
849 giraffe_image_delete(rscience);
850
851 return 1;
852 }
853
854
855 /*
856 * Spectrum extraction
857 */
858
859 if (slight_frame) {
860
861 filename = cpl_frame_get_filename(slight_frame);
862
863
864 slight = giraffe_image_new(CPL_TYPE_DOUBLE);
865 status = giraffe_image_load(slight, filename, 0);
866
867 if (status) {
868 cpl_msg_error(_id, "Cannot load scattered light model from '%s'. "
869 "Aborting ...", filename);
870
871 giraffe_image_delete(slight);
872
873 giraffe_localization_destroy(localization);
874
875 if (bpixel) {
876 giraffe_image_delete(bpixel);
877 bpixel = NULL;
878 }
879
880 giraffe_table_delete(fibers);
881 giraffe_image_delete(rscience);
882
883 return 1;
884
885 }
886
887 }
888
889
890 extract_config = giraffe_extract_config_create(config);
891
892 if ((extract_config->emethod == GIEXTRACT_OPTIMAL) ||
893 (extract_config->emethod == GIEXTRACT_HORNE)) {
894
895 if (psfdata_frame == NULL) {
896
897 const cxchar* emethod = "Optimal";
898
899 if (extract_config->emethod == GIEXTRACT_HORNE) {
900 emethod = "Horne";
901 }
902
903 cpl_msg_error(_id, "%s spectrum extraction requires PSF "
904 "profile data. Aborting ...", emethod);
905
906 giraffe_extract_config_destroy(extract_config);
907 extract_config = NULL;
908
909 if (slight != NULL) {
910 giraffe_image_delete(slight);
911 slight = NULL;
912 }
913
914 giraffe_localization_destroy(localization);
915 localization = NULL;
916
917 if (bpixel) {
918 giraffe_image_delete(bpixel);
919 bpixel = NULL;
920 }
921
922 giraffe_table_delete(fibers);
923 fibers = NULL;
924
925 giraffe_image_delete(rscience);
926 rscience = NULL;
927
928 return 1;
929
930 }
931 else {
932
933 filename = cpl_frame_get_filename(psfdata_frame);
934
935 localization->psf = giraffe_psfdata_new();
936 status = giraffe_psfdata_load(localization->psf, filename);
937
938 if (status) {
939 cpl_msg_error(_id, "Cannot load PSF profile data frame from "
940 "'%s'. Aborting ...", filename);
941
942 giraffe_extract_config_destroy(extract_config);
943 extract_config = NULL;
944
945 if (slight != NULL) {
946 giraffe_image_delete(slight);
947 slight = NULL;
948 }
949
950 giraffe_localization_destroy(localization);
951 localization = NULL;
952
953 if (bpixel) {
954 giraffe_image_delete(bpixel);
955 bpixel = NULL;
956 }
957
958 giraffe_table_delete(fibers);
959 fibers = NULL;
960
961 giraffe_image_delete(rscience);
962 rscience = NULL;
963
964 return 1;
965
966 }
967
968 }
969
970 }
971
972
973 extraction = giraffe_extraction_new();
974
975 status = giraffe_extract_spectra(extraction, rscience, fibers,
976 localization, bpixel, slight,
977 extract_config);
978
979 if (status) {
980 cpl_msg_error(_id, "Spectrum extraction failed! Aborting ...");
981
982 giraffe_extraction_destroy(extraction);
983 giraffe_extract_config_destroy(extract_config);
984
985 giraffe_image_delete(slight);
986
987 giraffe_localization_destroy(localization);
988
989 if (bpixel) {
990 giraffe_image_delete(bpixel);
991 bpixel = NULL;
992 }
993
994 giraffe_table_delete(fibers);
995 giraffe_image_delete(rscience);
996
997 return 1;
998 }
999
1000 giraffe_image_delete(slight);
1001 slight = NULL;
1002
1003 if (bpixel) {
1004 giraffe_image_delete(bpixel);
1005 bpixel = NULL;
1006 }
1007
1008 giraffe_image_delete(rscience);
1009 rscience = NULL;
1010
1011 giraffe_extract_config_destroy(extract_config);
1012
1013
1014 /*
1015 * Apply flat field and apply the relative fiber transmission correction.
1016 */
1017
1018 flat_config = giraffe_flat_config_create(config);
1019
1020 if (flat_config->load == TRUE) {
1021
1022 cpl_frame* flat_frame = NULL;
1023
1024 GiImage* flat = NULL;
1025
1026
1027 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTSPECTRA);
1028
1029 if (flat_frame == NULL) {
1030 cpl_msg_error(_id, "Missing flat field spectra frame!");
1031
1032 giraffe_flat_config_destroy(flat_config);
1033
1034 giraffe_extraction_destroy(extraction);
1035 giraffe_localization_destroy(localization);
1036
1037 giraffe_table_delete(wcalcoeff);
1038
1039 giraffe_table_delete(grating);
1040 giraffe_table_delete(fibers);
1041
1042 return 1;
1043 }
1044
1045 filename = cpl_frame_get_filename(flat_frame);
1046
1047 flat = giraffe_image_new(CPL_TYPE_DOUBLE);
1048 status = giraffe_image_load(flat, filename, 0);
1049
1050 if (status) {
1051 cpl_msg_error(_id, "Cannot load flat field spectra from '%s'. "
1052 "Aborting ...", filename);
1053
1054 giraffe_image_delete(flat);
1055
1056 giraffe_flat_config_destroy(flat_config);
1057
1058 giraffe_extraction_destroy(extraction);
1059 giraffe_localization_destroy(localization);
1060
1061 giraffe_table_delete(wcalcoeff);
1062
1063 giraffe_table_delete(grating);
1064 giraffe_table_delete(fibers);
1065
1066 return 1;
1067 }
1068
1069 if (flat_config->apply == TRUE) {
1070
1071 GiImage* errors = NULL;
1072
1073
1074 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTERRORS);
1075
1076 if (flat_frame == NULL) {
1077 cpl_msg_warning(_id, "Missing flat field spectra errors "
1078 "frame!");
1079 }
1080 else {
1081
1082 filename = cpl_frame_get_filename(flat_frame);
1083
1084 errors = giraffe_image_new(CPL_TYPE_DOUBLE);
1085 status = giraffe_image_load(errors, filename, 0);
1086
1087 if (status) {
1088 cpl_msg_error(_id, "Cannot load flat field spectra "
1089 "errors from '%s'. Aborting ...",
1090 filename);
1091
1092 giraffe_image_delete(errors);
1093 giraffe_image_delete(flat);
1094
1095 giraffe_flat_config_destroy(flat_config);
1096
1097 giraffe_extraction_destroy(extraction);
1098 giraffe_localization_destroy(localization);
1099
1100 giraffe_table_delete(wcalcoeff);
1101
1102 giraffe_table_delete(grating);
1103 giraffe_table_delete(fibers);
1104
1105 return 1;
1106 }
1107
1108 }
1109
1110 cpl_msg_info(_id, "Applying flat field correction ...");
1111
1112 status = giraffe_flat_apply(extraction, fibers, flat, errors,
1113 flat_config);
1114
1115 if (status) {
1116 cpl_msg_error(_id, "Flat field correction failed! "
1117 "Aborting ...");
1118
1119 giraffe_image_delete(errors);
1120 giraffe_image_delete(flat);
1121
1122 giraffe_flat_config_destroy(flat_config);
1123
1124 giraffe_extraction_destroy(extraction);
1125 giraffe_localization_destroy(localization);
1126
1127 giraffe_table_delete(wcalcoeff);
1128
1129 giraffe_table_delete(grating);
1130 giraffe_table_delete(fibers);
1131
1132 return 1;
1133 }
1134
1135 giraffe_image_delete(errors);
1136 errors = NULL;
1137
1138 }
1139
1140 if (flat_config->transmission == TRUE) {
1141
1142 const cxchar* _filename = cpl_frame_get_filename(flat_frame);
1143
1144 GiTable* _fibers = NULL;
1145
1146
1147 cpl_msg_info(_id, "Loading fiber setup for frame '%s'.",
1148 _filename);
1149
1150 _fibers = giraffe_fiberlist_load(_filename, 1, "FIBER_SETUP");
1151
1152 if (!_fibers) {
1153 cpl_msg_error(_id, "Cannot create fiber setup for "
1154 "frame '%s'! Aborting ...", _filename);
1155
1156 giraffe_image_delete(flat);
1157
1158 giraffe_flat_config_destroy(flat_config);
1159
1160 giraffe_extraction_destroy(extraction);
1161 giraffe_localization_destroy(localization);
1162
1163 giraffe_table_delete(wcalcoeff);
1164
1165 giraffe_table_delete(grating);
1166 giraffe_table_delete(fibers);
1167
1168 return 1;
1169 }
1170
1171 cpl_msg_info(_id, "Applying relative fiber transmission "
1172 "correction");
1173
1174 status = giraffe_transmission_setup(fibers, _fibers);
1175 giraffe_table_delete(_fibers);
1176
1177 if (status == 0) {
1178 status = giraffe_transmission_apply(extraction, fibers);
1179 }
1180
1181 if (status) {
1182
1183 cpl_msg_error(_id, "Relative transmission correction failed! "
1184 "Aborting ...");
1185
1186 giraffe_image_delete(flat);
1187
1188 giraffe_flat_config_destroy(flat_config);
1189
1190 giraffe_extraction_destroy(extraction);
1191 giraffe_localization_destroy(localization);
1192
1193 giraffe_table_delete(wcalcoeff);
1194
1195 giraffe_table_delete(grating);
1196 giraffe_table_delete(fibers);
1197
1198 return 1;
1199
1200 }
1201
1202 }
1203
1204 giraffe_image_delete(flat);
1205
1206 }
1207
1208 giraffe_flat_config_destroy(flat_config);
1209
1210
1211 /*
1212 * Save the spectrum extraction results and register them as
1213 * products.
1214 */
1215
1216 cpl_msg_info(_id, "Writing extracted spectra ...");
1217
1218 /* Extracted spectra */
1219
1220 giraffe_image_add_info(extraction->spectra, &info, set);
1221
1222 cpl_propertylist* extprop = giraffe_image_get_properties(extraction->spectra);
1223
1224 giraffe_qc_update_sci_props(extprop, fibers);
1225
1226
1227 sext_frame = giraffe_frame_create_image(extraction->spectra,
1228 GIFRAME_SCIENCE_EXTSPECTRA,
1229 CPL_FRAME_LEVEL_FINAL,
1230 TRUE, TRUE);
1231
1232 if (sext_frame == NULL) {
1233 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1234
1235 giraffe_extraction_destroy(extraction);
1236 giraffe_localization_destroy(localization);
1237
1238 giraffe_table_delete(wcalcoeff);
1239
1240 giraffe_table_delete(grating);
1241 giraffe_table_delete(fibers);
1242
1243 return 1;
1244 }
1245
1246 status = giraffe_fiberlist_attach(sext_frame, fibers);
1247
1248 if (status) {
1249 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1250 "Aborting ...", cpl_frame_get_filename(sext_frame));
1251
1252 cpl_frame_delete(sext_frame);
1253
1254 giraffe_extraction_destroy(extraction);
1255 giraffe_localization_destroy(localization);
1256
1257 giraffe_table_delete(wcalcoeff);
1258
1259 giraffe_table_delete(grating);
1260 giraffe_table_delete(fibers);
1261
1262 return 1;
1263 }
1264
1265 cpl_frameset_insert(set, sext_frame);
1266
1267 /* Extracted spectra errors */
1268
1269
1270
1271 cpl_propertylist* exterrprop = giraffe_image_get_properties(extraction->error);
1272
1273 giraffe_qc_update_sci_props(exterrprop, fibers);
1274
1275
1276 giraffe_image_add_info(extraction->error, &info, set);
1277
1278 sext_frame = giraffe_frame_create_image(extraction->error,
1279 GIFRAME_SCIENCE_EXTERRORS,
1280 CPL_FRAME_LEVEL_FINAL,
1281 TRUE, TRUE);
1282
1283 if (sext_frame == NULL) {
1284 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1285
1286 giraffe_extraction_destroy(extraction);
1287 giraffe_localization_destroy(localization);
1288
1289 giraffe_table_delete(wcalcoeff);
1290
1291 giraffe_table_delete(grating);
1292 giraffe_table_delete(fibers);
1293
1294 return 1;
1295 }
1296
1297 status = giraffe_fiberlist_attach(sext_frame, fibers);
1298
1299 if (status) {
1300 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1301 "Aborting ...", cpl_frame_get_filename(sext_frame));
1302
1303 cpl_frame_delete(sext_frame);
1304
1305 giraffe_extraction_destroy(extraction);
1306 giraffe_localization_destroy(localization);
1307
1308 giraffe_table_delete(wcalcoeff);
1309
1310 giraffe_table_delete(grating);
1311 giraffe_table_delete(fibers);
1312
1313 return 1;
1314 }
1315
1316 cpl_frameset_insert(set, sext_frame);
1317
1318 /* Extracted spectra pixels */
1319
1320 if (extraction->npixels != NULL) {
1321
1322 cpl_propertylist* extpixprop = giraffe_image_get_properties(extraction->npixels);
1323
1324 giraffe_qc_update_sci_props(extpixprop, fibers);
1325
1326 giraffe_image_add_info(extraction->npixels, &info, set);
1327
1328 sext_frame = giraffe_frame_create_image(extraction->npixels,
1329 GIFRAME_SCIENCE_EXTPIXELS,
1330 CPL_FRAME_LEVEL_FINAL,
1331 TRUE, TRUE);
1332
1333 if (sext_frame == NULL) {
1334 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1335
1336 giraffe_extraction_destroy(extraction);
1337 giraffe_localization_destroy(localization);
1338
1339 giraffe_table_delete(wcalcoeff);
1340
1341 giraffe_table_delete(grating);
1342 giraffe_table_delete(fibers);
1343
1344 return 1;
1345 }
1346
1347 status = giraffe_fiberlist_attach(sext_frame, fibers);
1348
1349 if (status) {
1350 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1351 "Aborting ...", cpl_frame_get_filename(sext_frame));
1352
1353 cpl_frame_delete(sext_frame);
1354
1355 giraffe_extraction_destroy(extraction);
1356 giraffe_localization_destroy(localization);
1357
1358 giraffe_table_delete(wcalcoeff);
1359
1360 giraffe_table_delete(grating);
1361 giraffe_table_delete(fibers);
1362
1363 return 1;
1364 }
1365
1366 cpl_frameset_insert(set, sext_frame);
1367
1368 }
1369
1370 /* Extracted spectra centroids */
1371
1372 giraffe_image_add_info(extraction->centroid, &info, set);
1373
1374 sext_frame = giraffe_frame_create_image(extraction->centroid,
1375 GIFRAME_SCIENCE_EXTTRACE,
1376 CPL_FRAME_LEVEL_FINAL,
1377 TRUE, TRUE);
1378
1379 if (sext_frame == NULL) {
1380 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1381
1382 giraffe_extraction_destroy(extraction);
1383 giraffe_localization_destroy(localization);
1384
1385 giraffe_table_delete(wcalcoeff);
1386
1387 giraffe_table_delete(grating);
1388 giraffe_table_delete(fibers);
1389
1390 return 1;
1391 }
1392
1393 status = giraffe_fiberlist_attach(sext_frame, fibers);
1394
1395 if (status) {
1396 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1397 "Aborting ...", cpl_frame_get_filename(sext_frame));
1398
1399 cpl_frame_delete(sext_frame);
1400
1401 giraffe_extraction_destroy(extraction);
1402 giraffe_localization_destroy(localization);
1403
1404 giraffe_table_delete(wcalcoeff);
1405
1406 giraffe_table_delete(grating);
1407 giraffe_table_delete(fibers);
1408
1409 return 1;
1410 }
1411
1412 cpl_frameset_insert(set, sext_frame);
1413
1414 /* Extraction model spectra */
1415
1416 if (extraction->model != NULL) {
1417
1418 giraffe_image_add_info(extraction->model, &info, set);
1419
1420 sext_frame = giraffe_frame_create_image(extraction->model,
1421 GIFRAME_SCIENCE_EXTMODEL,
1422 CPL_FRAME_LEVEL_FINAL,
1423 TRUE, TRUE);
1424
1425 if (sext_frame == NULL) {
1426 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1427
1428 giraffe_extraction_destroy(extraction);
1429 giraffe_localization_destroy(localization);
1430
1431 giraffe_table_delete(wcalcoeff);
1432
1433 giraffe_table_delete(grating);
1434 giraffe_table_delete(fibers);
1435
1436 return 1;
1437 }
1438
1439 status = giraffe_fiberlist_attach(sext_frame, fibers);
1440
1441 if (status != 0) {
1442 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1443 "Aborting ...", cpl_frame_get_filename(sext_frame));
1444
1445 cpl_frame_delete(sext_frame);
1446
1447 giraffe_extraction_destroy(extraction);
1448 giraffe_localization_destroy(localization);
1449
1450 giraffe_table_delete(wcalcoeff);
1451
1452 giraffe_table_delete(grating);
1453 giraffe_table_delete(fibers);
1454
1455 return 1;
1456 }
1457
1458 cpl_frameset_insert(set, sext_frame);
1459
1460 }
1461
1462
1463 /*
1464 * Load dispersion solution
1465 */
1466
1467
1468 filename = (cxchar *)cpl_frame_get_filename(wcal_frame);
1469
1470 tempes = cpl_errorstate_get();
1471
1472 const char qcdltcopy[] = "^(ESO INS TEMP53 VAL|MJD-OBS)$";
1473 cpl_propertylist * qcdltlist = cpl_propertylist_load_regexp(filename, 0,
1474 qcdltcopy, 0);
1475 cpl_errorstate_set(tempes);
1476
1477 wcalcoeff = giraffe_table_new();
1478 status = giraffe_table_load(wcalcoeff, filename, 1, NULL);
1479
1480 if (status) {
1481 cpl_msg_error(_id, "Cannot load dispersion solution from "
1482 "'%s'. Aborting ...", filename);
1483
1484 giraffe_extraction_destroy(extraction);
1485 giraffe_localization_destroy(localization);
1486
1487 giraffe_table_delete(wcalcoeff);
1488
1489 giraffe_table_delete(grating);
1490 giraffe_table_delete(fibers);
1491
1492 return 1;
1493 }
1494
1495
1496 /*
1497 * Load grating data
1498 */
1499
1500 filename = (cxchar *)cpl_frame_get_filename(grating_frame);
1501
1502
1503 grating = giraffe_table_new();
1504 status = giraffe_table_load(grating, filename, 1, NULL);
1505
1506 if (status) {
1507 cpl_msg_error(_id, "Cannot load grating data from '%s'. "
1508 "Aborting ...", filename);
1509
1510 giraffe_extraction_destroy(extraction);
1511 giraffe_localization_destroy(localization);
1512
1513 giraffe_table_delete(wcalcoeff);
1514
1515 giraffe_table_delete(grating);
1516 giraffe_table_delete(fibers);
1517
1518 return 1;
1519 }
1520
1521
1522 /*
1523 * Load slit geometry data
1524 */
1525
1526
1527 filename = (cxchar *)cpl_frame_get_filename(slit_frame);
1528
1529 slitgeometry = giraffe_slitgeometry_load(fibers, filename, 1, NULL);
1530
1531 if (slitgeometry == NULL) {
1532 cpl_msg_error(_id, "Cannot load slit geometry data from '%s'. "
1533 "Aborting ...", filename);
1534
1535 giraffe_table_delete(wcalcoeff);
1536
1537 giraffe_extraction_destroy(extraction);
1538 giraffe_localization_destroy(localization);
1539
1540 giraffe_table_delete(wcalcoeff);
1541
1542 giraffe_table_delete(grating);
1543 giraffe_table_delete(fibers);
1544
1545 return 1;
1546 }
1547 else {
1548
1549 /*
1550 * Check whether the contains the positions for all fibers
1551 * provided by the fiber setup. If this is not the case
1552 * this is an error.
1553 */
1554
1555 if (giraffe_fiberlist_compare(slitgeometry, fibers) != 1) {
1556 cpl_msg_error(_id, "Slit geometry data from '%s' is not "
1557 "applicable for current fiber setup! "
1558 "Aborting ...", filename);
1559
1560 giraffe_table_delete(slitgeometry);
1561 giraffe_table_delete(wcalcoeff);
1562
1563 giraffe_extraction_destroy(extraction);
1564 giraffe_localization_destroy(localization);
1565
1566 giraffe_table_delete(wcalcoeff);
1567
1568 giraffe_table_delete(grating);
1569 giraffe_table_delete(fibers);
1570
1571 return 1;
1572 }
1573
1574 }
1575
1576
1577
1578 /*
1579 * Spectrum rebinning
1580 */
1581
1582 cpl_msg_info(_id, "Spectrum rebinning");
1583
1584 rebin_config = giraffe_rebin_config_create(config);
1585
1586 rebinning = giraffe_rebinning_new();
1587
1588 status = giraffe_rebin_spectra(rebinning, extraction, fibers,
1589 localization, grating, slitgeometry,
1590 wcalcoeff, rebin_config);
1591
1592 if (status) {
1593 cpl_msg_error(_id, "Rebinning of science spectra failed! Aborting...");
1594
1595 giraffe_rebinning_destroy(rebinning);
1596
1597 giraffe_extraction_destroy(extraction);
1598 giraffe_localization_destroy(localization);
1599
1600 giraffe_table_delete(wcalcoeff);
1601
1602 giraffe_table_delete(slitgeometry);
1603 giraffe_table_delete(grating);
1604 giraffe_table_delete(fibers);
1605
1606 giraffe_rebin_config_destroy(rebin_config);
1607
1608 return 1;
1609
1610 }
1611
1612
1613 /*
1614 * Optionally compute and apply spectral shifts from the simultaneous
1615 * calibration fibers. This is only done if the simultaneous calibration
1616 * fibers were used.
1617 */
1618
1619 p = cpl_parameterlist_find(config, "giraffe.siwc.apply");
1620 cx_assert(p != NULL);
1621
1622 siwc = cpl_parameter_get_bool(p);
1623 p = NULL;
1624
1625 properties = giraffe_image_get_properties(rebinning->spectra);
1626 cx_assert(properties != NULL);
1627
1628
1629 if (cpl_propertylist_has(properties, GIALIAS_STSCTAL) == TRUE) {
1630 calsim = cpl_propertylist_get_bool(properties, GIALIAS_STSCTAL);
1631 }
1632
1633
1634 if ((siwc == TRUE) && (calsim == TRUE) && (linemask_frame != NULL)) {
1635
1636 GiTable* linemask = giraffe_table_new();
1637
1638 GiSGCalConfig* siwc_config = NULL;
1639
1640
1641 siwc_config = giraffe_sgcalibration_config_create(config);
1642
1643 if (siwc_config == NULL) {
1644
1645 giraffe_table_delete(linemask);
1646 linemask = NULL;
1647
1648 giraffe_rebinning_destroy(rebinning);
1649
1650 giraffe_extraction_destroy(extraction);
1651 giraffe_localization_destroy(localization);
1652
1653 giraffe_table_delete(wcalcoeff);
1654
1655 giraffe_table_delete(slitgeometry);
1656 giraffe_table_delete(grating);
1657 giraffe_table_delete(fibers);
1658
1659 giraffe_rebin_config_destroy(rebin_config);
1660
1661 return 1;
1662
1663 }
1664
1665 filename = cpl_frame_get_filename(linemask_frame);
1666
1667 status = giraffe_table_load(linemask, filename, 1, NULL);
1668
1669 if (status) {
1670 cpl_msg_error(_id, "Cannot load line reference mask from '%s'. "
1671 "Aborting ...", filename);
1672
1673 giraffe_sgcalibration_config_destroy(siwc_config);
1674 siwc_config = NULL;
1675
1676 giraffe_table_delete(linemask);
1677 linemask = NULL;
1678
1679 giraffe_rebinning_destroy(rebinning);
1680
1681 giraffe_extraction_destroy(extraction);
1682 giraffe_localization_destroy(localization);
1683
1684 giraffe_table_delete(wcalcoeff);
1685
1686 giraffe_table_delete(slitgeometry);
1687 giraffe_table_delete(grating);
1688 giraffe_table_delete(fibers);
1689
1690 giraffe_rebin_config_destroy(rebin_config);
1691
1692 return 1;
1693
1694 }
1695
1696
1697 status = giraffe_compute_offsets(fibers, rebinning, grating,
1698 linemask, siwc_config);
1699
1700 if (status != 0) {
1701 cpl_msg_error(_id, "Applying simultaneous wavelength "
1702 "calibration correction failed! Aborting...");
1703
1704 giraffe_sgcalibration_config_destroy(siwc_config);
1705 siwc_config = NULL;
1706
1707 giraffe_table_delete(linemask);
1708 linemask = NULL;
1709
1710 giraffe_rebinning_destroy(rebinning);
1711
1712 giraffe_extraction_destroy(extraction);
1713 giraffe_localization_destroy(localization);
1714
1715 giraffe_table_delete(wcalcoeff);
1716
1717 giraffe_table_delete(slitgeometry);
1718 giraffe_table_delete(grating);
1719 giraffe_table_delete(fibers);
1720
1721 giraffe_rebin_config_destroy(rebin_config);
1722
1723 return 1;
1724
1725 }
1726
1727 giraffe_sgcalibration_config_destroy(siwc_config);
1728 siwc_config = NULL;
1729
1730 giraffe_table_delete(linemask);
1731 linemask = NULL;
1732
1733 giraffe_rebinning_destroy(rebinning);
1734 rebinning = giraffe_rebinning_new();
1735
1736 status = giraffe_rebin_spectra(rebinning, extraction, fibers,
1737 localization, grating, slitgeometry,
1738 wcalcoeff, rebin_config);
1739
1740 if (status) {
1741 cpl_msg_error(_id, "Rebinning of science spectra failed! "
1742 "Aborting...");
1743
1744 giraffe_rebinning_destroy(rebinning);
1745
1746 giraffe_extraction_destroy(extraction);
1747 giraffe_localization_destroy(localization);
1748
1749 giraffe_table_delete(wcalcoeff);
1750
1751 giraffe_table_delete(slitgeometry);
1752 giraffe_table_delete(grating);
1753 giraffe_table_delete(fibers);
1754
1755 giraffe_rebin_config_destroy(rebin_config);
1756
1757 return 1;
1758
1759 }
1760
1761 }
1762
1763 giraffe_extraction_destroy(extraction);
1764 extraction = NULL;
1765
1766 giraffe_localization_destroy(localization);
1767 localization = NULL;
1768
1769 giraffe_rebin_config_destroy(rebin_config);
1770 rebin_config = NULL;
1771
1772
1773 /*
1774 * Compute barycentric correction for each object spectrum (fiber)
1775 */
1776
1777 status = giraffe_add_rvcorrection(fibers, rebinning->spectra);
1778
1779 switch (status) {
1780 case 0:
1781 {
1782 break;
1783 }
1784
1785 case 1:
1786 {
1787 cpl_msg_warning(_id, "Missing observation time properties! "
1788 "Barycentric correction computation "
1789 "skipped!");
1790 status = 0;
1791 break;
1792 }
1793 case 2:
1794 {
1795 cpl_msg_warning(_id, "Missing telescope location properties! "
1796 "Barycentric correction computation "
1797 "skipped!");
1798 status = 0;
1799 break;
1800 }
1801 case 3:
1802 {
1803 cpl_msg_warning(_id, "Object positions are not available "
1804 "Barycentric correction computation "
1805 "skipped!");
1806 status = 0;
1807 break;
1808 }
1809 default:
1810 {
1811 cpl_msg_error(_id, "Barycentric correction computation "
1812 "failed! Aborting...");
1813
1814 giraffe_rebinning_destroy(rebinning);
1815
1816 giraffe_table_delete(wcalcoeff);
1817
1818 giraffe_table_delete(slitgeometry);
1819 giraffe_table_delete(grating);
1820 giraffe_table_delete(fibers);
1821
1822 return 1;
1823 break;
1824 }
1825
1826 }
1827
1828
1829 /*
1830 * Save and register the results of the spectrum rebinning.
1831 */
1832
1833 /* Rebinned spectra */
1834
1835 /*
1836 * Add the QC parameters to the rebinning spectra
1837 */
1838
1839 tempes = cpl_errorstate_get();
1840
1841 cpl_propertylist* rbprop = giraffe_image_get_properties(rebinning->spectra);
1842
1843
1844 giraffe_propertylist_copy(rbprop, GIALIAS_WLSTART, rbprop,
1845 GIALIAS_BINWLMIN);
1846 giraffe_propertylist_copy(rbprop, GIALIAS_WLEND, rbprop,
1847 GIALIAS_BINWLMAX);
1848 giraffe_propertylist_copy(rbprop, GIALIAS_WLSTEP, rbprop,
1849 GIALIAS_BINSTEP);
1850
1851 double dlttemp = cpl_propertylist_get_double(rbprop, "ESO INS TEMP53 VAL");
1852 dlttemp -= cpl_propertylist_get_double(qcdltlist, "ESO INS TEMP53 VAL");
1853
1854 double dltdate = cpl_propertylist_get_double(rbprop, "MJD-OBS");
1855 dltdate -= cpl_propertylist_get_double(qcdltlist, "MJD-OBS");
1856
1857 cpl_propertylist_delete(qcdltlist);
1858
1859 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTEMP, dlttemp);
1860 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTIME, dltdate);
1861
1862
1863 cpl_errorstate_set(tempes);
1864
1865 giraffe_image_add_info(rebinning->spectra, &info, set);
1866
1867 rbin_frame = giraffe_frame_create_image(rebinning->spectra,
1868 GIFRAME_SCIENCE_RBNSPECTRA,
1869 CPL_FRAME_LEVEL_FINAL,
1870 TRUE, TRUE);
1871
1872 if (rbin_frame == NULL) {
1873 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1874
1875 giraffe_rebinning_destroy(rebinning);
1876
1877 giraffe_table_delete(wcalcoeff);
1878
1879 giraffe_table_delete(slitgeometry);
1880 giraffe_table_delete(grating);
1881 giraffe_table_delete(fibers);
1882
1883 return 1;
1884 }
1885
1886 status = giraffe_fiberlist_attach(rbin_frame, fibers);
1887
1888 if (status) {
1889 cpl_msg_error(_id, "Cannot attach fiber setup to local "
1890 "file '%s'! Aborting ...",
1891 cpl_frame_get_filename(rbin_frame));
1892
1893 giraffe_rebinning_destroy(rebinning);
1894 giraffe_table_delete(wcalcoeff);
1895
1896 giraffe_table_delete(slitgeometry);
1897 giraffe_table_delete(grating);
1898 giraffe_table_delete(fibers);
1899
1900 cpl_frame_delete(rbin_frame);
1901
1902 return 1;
1903 }
1904
1905 cpl_frameset_insert(set, rbin_frame);
1906 flux_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
1907
1908 /* Rebinned spectra errors */
1909
1910 tempes = cpl_errorstate_get();
1911
1912 cpl_propertylist* rberrprop = giraffe_image_get_properties(rebinning->errors);
1913
1914
1915 giraffe_propertylist_copy(rberrprop, GIALIAS_WLSTART, rberrprop,
1916 GIALIAS_BINWLMIN);
1917 giraffe_propertylist_copy(rberrprop, GIALIAS_WLEND, rberrprop,
1918 GIALIAS_BINWLMAX);
1919 giraffe_propertylist_copy(rberrprop, GIALIAS_WLSTEP, rberrprop,
1920 GIALIAS_BINSTEP);
1921
1922 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTEMP, dlttemp);
1923 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTIME, dltdate);
1924
1925
1926 giraffe_image_add_info(rebinning->errors, &info, set);
1927
1928 cpl_errorstate_set(tempes);
1929
1930 rbin_frame = giraffe_frame_create_image(rebinning->errors,
1931 GIFRAME_SCIENCE_RBNERRORS,
1932 CPL_FRAME_LEVEL_FINAL,
1933 TRUE, TRUE);
1934
1935 if (rbin_frame == NULL) {
1936 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1937
1938 giraffe_rebinning_destroy(rebinning);
1939
1940 giraffe_table_delete(wcalcoeff);
1941
1942 giraffe_table_delete(slitgeometry);
1943 giraffe_table_delete(grating);
1944 giraffe_table_delete(fibers);
1945 cpl_free(flux_filename);
1946
1947 return 1;
1948 }
1949
1950 status = giraffe_fiberlist_attach(rbin_frame, fibers);
1951
1952 if (status) {
1953 cpl_msg_error(_id, "Cannot attach fiber setup to local "
1954 "file '%s'! Aborting ...",
1955 cpl_frame_get_filename(rbin_frame));
1956
1957 giraffe_rebinning_destroy(rebinning);
1958
1959 giraffe_table_delete(wcalcoeff);
1960
1961 giraffe_table_delete(slitgeometry);
1962 giraffe_table_delete(grating);
1963 giraffe_table_delete(fibers);
1964
1965 cpl_frame_delete(rbin_frame);
1966 cpl_free(flux_filename);
1967
1968 return 1;
1969 }
1970
1971 cpl_frameset_insert(set, rbin_frame);
1972 err_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
1973
1974 properties = giraffe_image_get_properties(rebinning->spectra);
1975 mode = giraffe_get_mode(properties);
1976
1977 /*
1978 * Optionally generate spectra in Science Data Product (SDP) format.
1979 */
1980 p = cpl_parameterlist_find(config, "giraffe.sdp.format.generate");
1981 cx_assert(p != NULL);
1982 gensdp = cpl_parameter_get_bool(p);
1983 p = cpl_parameterlist_find(config, "giraffe.sdp.nassoc.keys");
1984 cx_assert(p != NULL);
1985 nassoc_keys = cpl_parameter_get_int(p);
1986 p = NULL;
1987 if (gensdp) {
1988 if (mode == GIMODE_MEDUSA) {
1989 status = _giraffe_make_sdp_spectra(flux_filename, err_filename,
1990 nassoc_keys, set, config, _id);
1991 if (status) {
1992 cpl_msg_error(_id, "Failed to generate spectra in Science Data"
1993 " Product format.");
1994
1995 giraffe_rebinning_destroy(rebinning);
1996
1997 giraffe_table_delete(wcalcoeff);
1998
1999 giraffe_table_delete(slitgeometry);
2000 giraffe_table_delete(grating);
2001 giraffe_table_delete(fibers);
2002
2003 cpl_free(flux_filename);
2004 cpl_free(err_filename);
2005
2006 return 1;
2007 }
2008 } else {
2009 cpl_msg_warning(_id, "Requested to generate SDP 1D spectra, but"
2010 " this is currently only supported for the MEDUSA"
2011 " mode. Skipping SDP generation.");
2012 }
2013 }
2014 cpl_free(flux_filename);
2015 cpl_free(err_filename);
2016
2017
2018 /*
2019 * Optional image and data cube construction (only for IFU and Argus)
2020 */
2021
2022 if (mode == GIMODE_IFU || mode == GIMODE_ARGUS) {
2023
2024 cpl_frame* rimg_frame = NULL;
2025
2026 GiFieldOfView* fov = NULL;
2027
2028 GiFieldOfViewConfig* fov_config = NULL;
2029
2030 GiFieldOfViewCubeFormat cube_format = GIFOV_FORMAT_ESO3D;
2031
2032
2033 fov_config = giraffe_fov_config_create(config);
2034
2035 cube_format = fov_config->format;
2036
2037
2038 cpl_msg_info(_id, "Reconstructing image and data cube from rebinned "
2039 "spectra ...");
2040
2041 fov = giraffe_fov_new();
2042
2043 status = giraffe_fov_build(fov, rebinning, fibers, wcalcoeff, grating,
2044 slitgeometry, fov_config);
2045
2046 if (status) {
2047
2048 if (status == -2) {
2049 cpl_msg_warning(_id, "No reconstructed image was built. "
2050 "Fiber list has no fiber position "
2051 "information.");
2052 }
2053 else {
2054 cpl_msg_error(_id, "Image reconstruction failed! Aborting...");
2055
2056 giraffe_fov_delete(fov);
2057 giraffe_rebinning_destroy(rebinning);
2058
2059 giraffe_table_delete(wcalcoeff);
2060
2061 giraffe_table_delete(slitgeometry);
2062 giraffe_table_delete(grating);
2063 giraffe_table_delete(fibers);
2064
2065 giraffe_fov_config_destroy(fov_config);
2066
2067 return 1;
2068 }
2069
2070 }
2071
2072 giraffe_fov_config_destroy(fov_config);
2073
2074
2075 /*
2076 * Save and register the results of the image reconstruction.
2077 */
2078
2079 /* Reconstructed image */
2080
2081 giraffe_image_add_info(fov->fov.spectra, &info, set);
2082
2083 rimg_frame = giraffe_frame_create_image(fov->fov.spectra,
2084 GIFRAME_SCIENCE_RCSPECTRA,
2085 CPL_FRAME_LEVEL_FINAL,
2086 TRUE, TRUE);
2087
2088 if (rimg_frame == NULL) {
2089 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2090
2091 giraffe_fov_delete(fov);
2092 giraffe_rebinning_destroy(rebinning);
2093
2094 giraffe_table_delete(wcalcoeff);
2095
2096 giraffe_table_delete(slitgeometry);
2097 giraffe_table_delete(grating);
2098 giraffe_table_delete(fibers);
2099
2100 return 1;
2101 }
2102
2103 cpl_frameset_insert(set, rimg_frame);
2104
2105
2106 /* Reconstructed image errors */
2107
2108 giraffe_image_add_info(fov->fov.errors, &info, set);
2109
2110 rimg_frame = giraffe_frame_create_image(fov->fov.errors,
2111 GIFRAME_SCIENCE_RCERRORS,
2112 CPL_FRAME_LEVEL_FINAL,
2113 TRUE, TRUE);
2114
2115 if (rimg_frame == NULL) {
2116 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2117
2118 giraffe_fov_delete(fov);
2119 giraffe_rebinning_destroy(rebinning);
2120
2121 giraffe_table_delete(wcalcoeff);
2122
2123 giraffe_table_delete(slitgeometry);
2124 giraffe_table_delete(grating);
2125 giraffe_table_delete(fibers);
2126
2127 return 1;
2128 }
2129
2130 cpl_frameset_insert(set, rimg_frame);
2131
2132
2133 /* Save data cubes according to format selection */
2134
2135 if (cube_format == GIFOV_FORMAT_SINGLE) {
2136
2137 /* Spectrum cube */
2138
2139 if (fov->cubes.spectra != NULL) {
2140
2141 cxint component = 0;
2142
2143 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes;
2144
2145
2146 properties = giraffe_image_get_properties(rebinning->spectra);
2147 properties = cpl_propertylist_duplicate(properties);
2148
2149 giraffe_add_frameset_info(properties, set, info.sequence);
2150
2151 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE_SPECTRA,
2152 CPL_FRAME_LEVEL_FINAL,
2153 properties,
2154 fov,
2155 &component,
2156 creator);
2157
2158 cpl_propertylist_delete(properties);
2159 properties = NULL;
2160
2161 if (rimg_frame == NULL) {
2162 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2163
2164 giraffe_fov_delete(fov);
2165 fov = NULL;
2166
2167 giraffe_rebinning_destroy(rebinning);
2168 rebinning = NULL;
2169
2170 giraffe_table_delete(wcalcoeff);
2171 wcalcoeff = NULL;
2172
2173 giraffe_table_delete(slitgeometry);
2174 slitgeometry = NULL;
2175
2176 giraffe_table_delete(grating);
2177 grating = NULL;
2178
2179 giraffe_table_delete(fibers);
2180 fibers = NULL;
2181
2182 return 1;
2183 }
2184
2185 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2186
2187 if (status != 0) {
2188 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2189 "file '%s'! Aborting ...",
2190 cpl_frame_get_filename(rimg_frame));
2191
2192 cpl_frame_delete(rimg_frame);
2193
2194 giraffe_fov_delete(fov);
2195 fov = NULL;
2196
2197 giraffe_rebinning_destroy(rebinning);
2198 rebinning = NULL;
2199
2200 giraffe_table_delete(wcalcoeff);
2201 wcalcoeff = NULL;
2202
2203 giraffe_table_delete(slitgeometry);
2204 slitgeometry = NULL;
2205
2206 giraffe_table_delete(grating);
2207 grating = NULL;
2208
2209 giraffe_table_delete(fibers);
2210 fibers = NULL;
2211
2212 return 1;
2213 }
2214
2215 cpl_frameset_insert(set, rimg_frame);
2216
2217 }
2218
2219 /* Error cube */
2220
2221 if (fov->cubes.errors != NULL) {
2222
2223 cxint component = 1;
2224
2225 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes;
2226
2227
2228 properties = giraffe_image_get_properties(rebinning->errors);
2229 properties = cpl_propertylist_duplicate(properties);
2230
2231 giraffe_add_frameset_info(properties, set, info.sequence);
2232
2233 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE_ERRORS,
2234 CPL_FRAME_LEVEL_FINAL,
2235 properties,
2236 fov,
2237 &component,
2238 creator);
2239
2240 cpl_propertylist_delete(properties);
2241 properties = NULL;
2242
2243 if (rimg_frame == NULL) {
2244 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2245
2246 giraffe_fov_delete(fov);
2247 fov = NULL;
2248
2249 giraffe_rebinning_destroy(rebinning);
2250 rebinning = NULL;
2251
2252 giraffe_table_delete(wcalcoeff);
2253 wcalcoeff = NULL;
2254
2255 giraffe_table_delete(slitgeometry);
2256 slitgeometry = NULL;
2257
2258 giraffe_table_delete(grating);
2259 grating = NULL;
2260
2261 giraffe_table_delete(fibers);
2262 fibers = NULL;
2263
2264 return 1;
2265 }
2266
2267 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2268
2269 if (status != 0) {
2270 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2271 "file '%s'! Aborting ...",
2272 cpl_frame_get_filename(rimg_frame));
2273
2274 cpl_frame_delete(rimg_frame);
2275
2276 giraffe_fov_delete(fov);
2277 fov = NULL;
2278
2279 giraffe_rebinning_destroy(rebinning);
2280 rebinning = NULL;
2281
2282 giraffe_table_delete(wcalcoeff);
2283 wcalcoeff = NULL;
2284
2285 giraffe_table_delete(slitgeometry);
2286 slitgeometry = NULL;
2287
2288 giraffe_table_delete(grating);
2289 grating = NULL;
2290
2291 giraffe_table_delete(fibers);
2292 fibers = NULL;
2293
2294 return 1;
2295 }
2296
2297 cpl_frameset_insert(set, rimg_frame);
2298 }
2299
2300 }
2301 else {
2302
2303 /* Data Cube (ESO 3D format) */
2304
2305 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes_eso3d;
2306
2307 properties = giraffe_image_get_properties(rebinning->spectra);
2308 properties = cpl_propertylist_duplicate(properties);
2309
2310 giraffe_add_frameset_info(properties, set, info.sequence);
2311
2312 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE,
2313 CPL_FRAME_LEVEL_FINAL,
2314 properties,
2315 fov,
2316 NULL,
2317 creator);
2318
2319 cpl_propertylist_delete(properties);
2320 properties = NULL;
2321
2322 if (rimg_frame == NULL) {
2323 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2324
2325 giraffe_fov_delete(fov);
2326 fov = NULL;
2327
2328 giraffe_rebinning_destroy(rebinning);
2329 rebinning = NULL;
2330
2331 giraffe_table_delete(wcalcoeff);
2332 wcalcoeff = NULL;
2333
2334 giraffe_table_delete(slitgeometry);
2335 slitgeometry = NULL;
2336
2337 giraffe_table_delete(grating);
2338 grating = NULL;
2339
2340 giraffe_table_delete(fibers);
2341 fibers = NULL;
2342
2343 return 1;
2344 }
2345
2346 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2347
2348 if (status != 0) {
2349 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2350 "file '%s'! Aborting ...",
2351 cpl_frame_get_filename(rimg_frame));
2352
2353 cpl_frame_delete(rimg_frame);
2354
2355 giraffe_fov_delete(fov);
2356 fov = NULL;
2357
2358 giraffe_rebinning_destroy(rebinning);
2359 rebinning = NULL;
2360
2361 giraffe_table_delete(wcalcoeff);
2362 wcalcoeff = NULL;
2363
2364 giraffe_table_delete(slitgeometry);
2365 slitgeometry = NULL;
2366
2367 giraffe_table_delete(grating);
2368 grating = NULL;
2369
2370 giraffe_table_delete(fibers);
2371 fibers = NULL;
2372
2373 return 1;
2374 }
2375
2376 cpl_frameset_insert(set, rimg_frame);
2377
2378 }
2379
2380 giraffe_fov_delete(fov);
2381 fov = NULL;
2382
2383 }
2384
2385
2386 /*
2387 * Cleanup
2388 */
2389
2390 giraffe_table_delete(wcalcoeff);
2391
2392 giraffe_table_delete(slitgeometry);
2393 giraffe_table_delete(grating);
2394 giraffe_table_delete(fibers);
2395
2396 giraffe_rebinning_destroy(rebinning);
2397
2398 return 0;
2399
2400}
2401
2402
2403/*
2404 * Build table of contents, i.e. the list of available plugins, for
2405 * this module. This function is exported.
2406 */
2407
2408int
2409cpl_plugin_get_info(cpl_pluginlist* list)
2410{
2411
2412 cpl_recipe* recipe = cx_calloc(1, sizeof *recipe);
2413 cpl_plugin* plugin = &recipe->interface;
2414
2415
2416 cpl_plugin_init(plugin,
2417 CPL_PLUGIN_API,
2418 GIRAFFE_BINARY_VERSION,
2419 CPL_PLUGIN_TYPE_RECIPE,
2420 "giscience",
2421 "Process a science observation.",
2422 "For detailed information please refer to the "
2423 "GIRAFFE pipeline user manual.\nIt is available at "
2424 "http://www.eso.org/pipelines.",
2425 "Giraffe Pipeline",
2426 PACKAGE_BUGREPORT,
2427 giraffe_get_license(),
2428 giscience_create,
2429 giscience_exec,
2430 giscience_destroy);
2431
2432 cpl_pluginlist_append(list, plugin);
2433
2434 return 0;
2435
2436}
2437
2438
2439/* Structure of a lookup table entry for the LUT used to get values for
2440 * SPEC_RES. */
2441typedef struct _giraffe_lut_entry {
2442 const char* expmode;
2443 double specres;
2444 double lamrms; /* given in (px), to convert to (nm) one needs:
2445 lamrms * spec_length / 4100 */
2446 double spec_length;
2447 int lamnlin;
2448} giraffe_lut_entry;
2449
2450
2451#ifndef NDEBUG
2452
2457static cpl_boolean _giraffe_lut_is_sorted(const giraffe_lut_entry* lut,
2458 size_t nentries)
2459{
2460 size_t i;
2461 if (nentries < 2) return CPL_TRUE;
2462 for (i = 0; i < nentries - 1; ++i) {
2463 if (strcmp(lut[i].expmode, lut[i+1].expmode) >= 0) {
2464 return CPL_FALSE;
2465 }
2466 }
2467 return CPL_TRUE;
2468}
2469
2470#endif /* NDEBUG */
2471
2472
2480static const giraffe_lut_entry* _giraffe_find_lut_entry(const char* expmode)
2481{
2482 static giraffe_lut_entry lut[] = {
2483 /* INS_EXP_MODE lambda LAMRMS spec_length LAMNLIN
2484 * R = ------------- (px) (nm) line count
2485 * delta(lambda)
2486 */
2487 {"H379.", 25000, 0.2250, 20.0, 60},
2488 {"H379.0", 25000, 0.2250, 20.0, 60},
2489 {"H395.8", 22000, 0.1913, 21.1, 53},
2490 {"H412.4", 30000, 0.1326, 22.3, 48},
2491 {"H429.7", 23000, 0.1471, 23.5, 67},
2492 {"H447.1", 20000, 0.0906, 24.9, 63},
2493 {"H447.1A", 20000, 0.0906, 24.9, 63},
2494 {"H447.1B", 31000, 0.1297, 23.5, 58},
2495 {"H465.6", 23000, 0.1573, 22.4, 57},
2496 {"H484.5", 19000, 0.1175, 23.5, 57},
2497 {"H484.5A", 19000, 0.1175, 23.5, 57},
2498 {"H484.5B", 33000, 0.0907, 24.6, 61},
2499 {"H504.8", 22000, 0.1726, 25.2, 56},
2500 {"H525.8", 17000, 0.1397, 25.8, 49},
2501 {"H525.8A", 17000, 0.1397, 25.8, 49},
2502 {"H525.8B", 29000, 0.2014, 26.4, 44},
2503 {"H548.8", 20000, 0.2389, 26.9, 51},
2504 {"H572.8", 27000, 0.1844, 27.5, 49},
2505 {"H599.3", 18000, 0.1683, 28.3, 57},
2506 {"H627.3", 24000, 0.1268, 29.0, 50},
2507 {"H651.5", 17000, 0.1185, 30.0, 42},
2508 {"H651.5A", 17000, 0.1185, 30.0, 42},
2509 {"H651.5B", 35000, 0.1253, 31.5, 37},
2510 {"H665.", 17000, 0.2076, 33.0, 45},
2511 {"H665.0", 17000, 0.2076, 33.0, 45},
2512 {"H679.7", 19000, 0.1621, 34.5, 51},
2513 {"H710.5", 25000, 0.1495, 36.0, 48},
2514 {"H737.", 16000, 0.1456, 37.5, 47},
2515 {"H737.0", 16000, 0.1456, 37.5, 47},
2516 {"H737.0A", 16000, 0.1456, 37.5, 47},
2517 {"H737.0B", 35000, 0.1147, 39.5, 40},
2518 {"H769.1", 19000, 0.2811, 41.8, 35},
2519 {"H805.3", 14000, 0.2662, 42.4, 39},
2520 {"H805.3A", 14000, 0.2662, 42.4, 39},
2521 {"H805.3B", 25000, 0.2342, 42.9, 28},
2522 {"H836.6", 16000, 0.2032, 43.3, 21},
2523 {"H836.6A", 16000, 0.2032, 43.3, 21},
2524 {"H836.6B", 34000, 0.1073, 43.7, 14},
2525 {"H875.7", 18000, 0.2026, 44.3, 29},
2526 {"H920.5", 12000, 0.1568, 44.9, 32},
2527 {"H920.5A", 12000, 0.1568, 44.9, 32},
2528 {"H920.5B", 24000, 0.2531, 45.9, 28},
2529 {"L385.7", 7500, 0.3358, 58.0, 43},
2530 {"L427.2", 6300, 0.2152, 61.1, 62},
2531 {"L479.7", 7500, 0.1554, 71.0, 61},
2532 {"L543.1", 5800, 0.2065, 82.1, 58},
2533 {"L614.2", 6600, 0.1803, 79.0, 51},
2534 {"L682.2", 8100, 0.1843, 74.0, 50},
2535 {"L773.4", 5400, 0.1617, 94.0, 44},
2536 {"L881.7", 6600, 0.1614, 119.0, 29}
2537 };
2538 static const size_t nentries = sizeof(lut) / sizeof(giraffe_lut_entry);
2539 int low = 0; /* Bottom of search region. */
2540 int high = (int)nentries - 1; /* Top of search region. */
2541
2542 assert(_giraffe_lut_is_sorted(lut, nentries));
2543 assert(expmode != NULL);
2544
2545 /* Perform a binary search for the entry. */
2546 do {
2547 int mid = (low + high) >> 1; /* Find mid point of search range. */
2548 int result = strcmp(expmode, lut[mid].expmode);
2549 if (result == 0) {
2550 return &lut[mid];
2551 } else if (result < 0) {
2552 high = mid - 1;
2553 } else {
2554 low = mid + 1;
2555 }
2556 } while (high >= low);
2557 return NULL;
2558}
2559
2566static double _giraffe_lookup_specres(const char* expmode)
2567{
2568 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2569 if (entry == NULL) return NAN;
2570 return entry->specres;
2571}
2572
2579static double _giraffe_lookup_lamrms(const char* expmode)
2580{
2581 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2582 if (entry == NULL) return NAN;
2583 if (isnan(entry->lamrms) || isnan(entry->spec_length)) return NAN;
2584 return entry->lamrms * entry->spec_length / 4100.;
2585}
2586
2593static double _giraffe_lookup_lamnlin(const char* expmode)
2594{
2595 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2596 if (entry == NULL) return -1;
2597 return entry->lamnlin;
2598}
2599
2600
2611static cpl_type _giraffe_calc_wave_type(double crval2, double crpix2,
2612 double cdelt2, cpl_size naxis2)
2613{
2614 static const double errfrac = 0.02;
2615 static const double single_precision_digits = 7;
2616 double lo = (1.0 - crpix2) * cdelt2;
2617 double hi = ((double)naxis2 - crpix2) * cdelt2;
2618 double maxwave = crval2 + (hi > lo ? hi : lo);
2619 double binfrac = (maxwave != 0.0) ? fabs(cdelt2 / maxwave) : 0.0;
2620 if (binfrac * errfrac < pow(10, -single_precision_digits)) {
2621 return CPL_TYPE_DOUBLE;
2622 } else {
2623 return CPL_TYPE_FLOAT;
2624 }
2625}
2626
2627
2637static cpl_boolean _giraffe_ancillary_data_available(const char* filename,
2638 const GiTable* fibertable)
2639{
2640 cpl_table* tbl = giraffe_table_get(fibertable);
2641 cpl_size i;
2642 const char** spectypes = NULL;
2643
2644 assert(filename != NULL);
2645
2646 cpl_error_ensure(tbl != NULL, cpl_error_get_code(), return CPL_FALSE,
2647 "The fiber table is not available for '%s'.", filename);
2648
2649 spectypes = cpl_table_get_data_string_const(tbl, GIALIAS_COLUMN_TYPE);
2650 cpl_error_ensure(spectypes != NULL, cpl_error_get_code(), return CPL_FALSE,
2651 "Could not fetch the '%s' column from the fiber setup"
2652 " table in '%s'.", GIALIAS_COLUMN_TYPE, filename);
2653 /*
2654 * Step through the table and check for fiber types other than Medusa
2655 * fibers. Also the simultaneous calibration fibers are not considered
2656 * as ancillary spectra and are ignored.
2657 */
2658 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2659 if ((spectypes[i][0] != '\0') && (strcmp(spectypes[i], "M") != 0)) {
2660 return CPL_TRUE;
2661 }
2662 }
2663 return CPL_FALSE;
2664}
2665
2666
2686static cpl_error_code _giraffe_make_ancillary_file(cpl_frameset* allframes,
2687 const char* outputfile,
2688 const char* infilename,
2689 const GiImage* fluximage,
2690 const GiTable* fibertable)
2691{
2692 cpl_error_code error = CPL_ERROR_NONE;
2693 cxint retcode;
2694 cpl_frame* frame = NULL;
2695 cpl_image* srcimg = giraffe_image_get(fluximage);
2696 GiImage* image = NULL;
2697 GiTable* table = giraffe_table_duplicate(fibertable);
2698 cpl_image* img = NULL;
2699 cpl_table* tbl = giraffe_table_get(table);
2700 cpl_image* subimg = NULL;
2701 cpl_propertylist* comments = NULL;
2702 cpl_size ny, i;
2703 int* indices = NULL;
2704
2705 assert(allframes != NULL);
2706 assert(outputfile != NULL);
2707 assert(infilename != NULL);
2708
2709 cpl_error_ensure(srcimg != NULL && table != NULL && tbl != NULL,
2710 cpl_error_get_code(), goto cleanup,
2711 "The image or table are not available for '%s'.",
2712 infilename);
2713
2714 /* Setup a new frame for the output file. */
2715 frame = cpl_frame_new();
2716 error |= cpl_frame_set_filename(frame, outputfile);
2717 error |= cpl_frame_set_tag(frame, GIALIAS_ASSO_PROCATG_VALUE);
2718 error |= cpl_frame_set_type(frame, CPL_FRAME_TYPE_IMAGE);
2719 error |= cpl_frame_set_group(frame, CPL_FRAME_GROUP_PRODUCT);
2720 error |= cpl_frame_set_level(frame, CPL_FRAME_LEVEL_FINAL);
2721 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2722 "Failed to setup a new output frame for '%s'.",
2723 outputfile);
2724
2725 /* First step to filter out the science entries in the image and fiber setup
2726 * table is to go through the table entries, mark the entries to remove, and
2727 * delete the ones that are marked. i.e. unselect everything, select all
2728 * non-science spectra, ignoring the simultaneous calibration spectra,
2729 * invert the selection and remove everything that remains marked as
2730 * selected. */
2731 error |= cpl_table_unselect_all(tbl);
2732 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2733 "Failed to unselect all entries in fiber setup table from"
2734 " '%s'.", infilename);
2735 cpl_table_or_selected_string(tbl, GIALIAS_COLUMN_TYPE, CPL_NOT_EQUAL_TO,
2736 "M");
2737 cpl_table_and_selected_int(tbl, GIALIAS_COLUMN_RP, CPL_NOT_EQUAL_TO, -1);
2738 cpl_table_not_selected(tbl);
2739 error |= cpl_table_erase_selected(tbl);
2740 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2741 "Failed to erase selected entries in fiber setup table"
2742 " from '%s'.", infilename);
2743
2744 /* Create a new output image which is wide enough to store the data with the
2745 * stripped out spectra removed. */
2746 ny = cpl_image_get_size_y(srcimg);
2747 image = giraffe_image_create(cpl_image_get_type(srcimg),
2748 cpl_table_get_nrow(tbl), ny);
2749 img = giraffe_image_get(image);
2750 retcode = giraffe_image_set_properties(
2751 image, giraffe_image_get_properties(fluximage));
2752 cpl_error_ensure(image != NULL && img != NULL && retcode == 0,
2753 cpl_error_get_code(), goto cleanup,
2754 "Failed to create image for output file '%s'.",
2755 outputfile);
2756
2757 error |= cpl_propertylist_update_string(giraffe_image_get_properties(image),
2758 GIALIAS_PROCATG,
2759 GIALIAS_ASSO_PROCATG_VALUE);
2760 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2761 "Could not update keyword '%s' for output file '%s'.",
2762 GIALIAS_PROCATG, outputfile);
2763
2764
2765 error |= cpl_propertylist_update_string(giraffe_image_get_properties(image),
2766 GIALIAS_PRODCATG,
2767 GIALIAS_PRODCATG_MOSSKY);
2768 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2769 "Could not update keyword '%s' for output file '%s'.",
2770 GIALIAS_PRODCATG, outputfile);
2771
2772 /* Strip out extra comments which will be added by CPL anyway. */
2773 if (cpl_propertylist_has(giraffe_image_get_properties(image), "COMMENT")) {
2774 cpl_size ic;
2775 const char* comments_to_remove[] = {
2776 " FITS (Flexible Image Transport System) format is defined in"
2777 " 'Astronomy",
2778 " and Astrophysics', volume 376, page 359; bibcode: 2001A&A..."
2779 "376..359H",
2780 NULL
2781 };
2782 cpl_propertylist* props = giraffe_image_get_properties(image);
2783 comments = cpl_propertylist_new();
2784 error |= cpl_propertylist_copy_property_regexp(comments, props,
2785 "^COMMENT$", 0);
2786 cpl_propertylist_erase_regexp(props, "^COMMENT$", 0);
2787 for (ic = 0; ic < cpl_propertylist_get_size(comments); ++ic) {
2788 const char** cmnt_str;
2789 cpl_property* p = cpl_propertylist_get(comments, ic);
2790 for (cmnt_str = comments_to_remove; *cmnt_str != NULL; ++cmnt_str) {
2791 if (strcmp(cpl_property_get_string(p), *cmnt_str) == 0) {
2792 goto dont_add_comment;
2793 }
2794 }
2795 /* Add back comments that should not be removed. */
2796 error |= cpl_propertylist_append_property(props, p);
2797 dont_add_comment:
2798 /* Land up here if the comment was found in the comments_to_remove
2799 * list of strings. */
2800 ;
2801 }
2802 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2803 "Failed to cleanup comments in primary HDU for '%s'.",
2804 outputfile);
2805 cpl_propertylist_delete(comments);
2806 comments = NULL;
2807 }
2808
2809 /* We now have to relabel the index numbers in the fiber setup table and
2810 * copy corresponding image columns to the new image. */
2811 indices = cpl_table_get_data_int(tbl, GIALIAS_COLUMN_INDEX);
2812 cpl_error_ensure(indices != NULL, cpl_error_get_code(), goto cleanup,
2813 "Could not fetch the '%s' column from the fiber setup"
2814 " table in '%s'.", GIALIAS_COLUMN_INDEX, infilename);
2815 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2816 cpl_size oldindex = indices[i];
2817 cpl_size newindex = i+1;
2818 indices[i] = newindex;
2819 subimg = cpl_image_extract(srcimg, oldindex, 1, oldindex, ny);
2820 cpl_error_ensure(subimg != NULL, cpl_error_get_code(), goto cleanup,
2821 "Could not extract sub image from '%s' at column %"
2822 CPL_SIZE_FORMAT".", infilename, oldindex);
2823 error |= cpl_image_copy(img, subimg, newindex, 1);
2824 cpl_image_delete(subimg);
2825 subimg = NULL;
2826 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2827 "Could write sub image from '%s' at column %"
2828 CPL_SIZE_FORMAT" to new image in '%s' at column %"
2829 CPL_SIZE_FORMAT".", infilename, oldindex, outputfile,
2830 newindex);
2831 }
2832
2833 /* Now write the actual FITS file. */
2834 retcode = giraffe_image_save(image, outputfile);
2835 cpl_error_ensure(retcode == 0, cpl_error_get_code(), goto cleanup,
2836 "Failed to write image to file '%s'.", outputfile);
2837 retcode = giraffe_fiberlist_attach(frame, table);
2838 cpl_error_ensure(retcode == 0, cpl_error_get_code(), goto cleanup,
2839 "Failed to attach the fiber setup table to file '%s'.",
2840 outputfile);
2841
2842 /* Add the new frame to the output frame set for the ancillary file.
2843 * Note: this should be the last step so that we do not delete this frame
2844 * anymore once in the frame set. */
2845 error |= cpl_frameset_insert(allframes, frame);
2846 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2847 "Could not add a new frame to the frame list for '%s'.",
2848 outputfile);
2849
2850 giraffe_image_delete(image);
2851 giraffe_table_delete(table);
2852 return CPL_ERROR_NONE;
2853
2854cleanup:
2855 /* Error handling. Note: NULL pointer checks done by delete functions. */
2856 cpl_image_delete(subimg);
2857 giraffe_image_delete(image);
2858 giraffe_table_delete(table);
2859 cpl_frame_delete(frame);
2860 cpl_propertylist_delete(comments);
2861 return cpl_error_get_code();
2862}
2863
2864
2871static char* _giraffe_calc_format_string(cpl_size maxfiles)
2872{
2873 double ndigits = 1.0;
2874 if (maxfiles > 1) {
2875 /* Figure out how many digits must be printed to support a index number
2876 * as large as 'maxfiles'. */
2877 ndigits = ceil(log10((double)maxfiles + 1.0));
2878 }
2879 return cpl_sprintf("science_spectrum_%%0%.0f"CPL_SIZE_FORMAT".fits",
2880 ndigits);
2881}
2882
2883
2900static cxint _giraffe_make_sdp_spectra(const cxchar* flux_filename,
2901 const cxchar* err_filename,
2902 cxint nassoc_keys,
2903 cpl_frameset* allframes,
2904 const cpl_parameterlist* parlist,
2905 const cxchar* recipe_id)
2906{
2907 cxint result_code = 1;
2908 cxint errorcode;
2909 cpl_error_code error = CPL_ERROR_NONE;
2910 cpl_errorstate prestate;
2911 const char* ancillary_filename = "science_ancillary.fits";
2912 GiImage* fluximage = giraffe_image_new(CPL_TYPE_DOUBLE);
2913 GiImage* errimage = giraffe_image_new(CPL_TYPE_DOUBLE);
2914 GiTable* fibertable = NULL;
2915 const cxchar* fibertable_name = NULL;
2916 irplib_sdp_spectrum* spectrum = NULL;
2917 cpl_propertylist* extrakeys = cpl_propertylist_new();
2918 cpl_propertylist* tablekeys = cpl_propertylist_new();
2919 cpl_propertylist* props;
2920 char* pipe_id = cpl_sprintf("%s/%s", PACKAGE, VERSION);
2921 const char* dict_id = PRODUCT_DID;
2922 const cpl_frame* inherit = NULL;
2923 cpl_frameset* usedframes = NULL;
2924 cpl_frameset* rawframes = NULL;
2925 cpl_frameset_iterator* iterator = NULL;
2926 cpl_size nx, ny, i, filecount;
2927 double exptime = NAN;
2928 double mjdobs = NAN;
2929 double mjdend = NAN;
2930 double wavelmin = NAN;
2931 double wavelmax = NAN;
2932 double specbin = NAN;
2933 double crpix2 = NAN;
2934 double crval2 = NAN;
2935 double cdelt2 = NAN;
2936 const char* cunit2 = NULL;
2937 double specres;
2938 const char* expmode = NULL;
2939 char strbuf[64];
2940 const int* indices = NULL;
2941 const int* fps = NULL;
2942 const char** objects = NULL;
2943 const char** spectypes = NULL;
2944 const double* ras = NULL;
2945 const double* decs = NULL;
2946 const double* gcorr = NULL;
2947 const double* hcorr = NULL;
2948 const double* bcorr = NULL;
2949 char* formatstr = NULL;
2950 char* filename = NULL;
2951 cpl_type wavecoltype;
2952 cpl_array* refwavearray = NULL;
2953 cpl_array* array = NULL;
2954 float* data_float = NULL;
2955 double* data_double = NULL;
2956 cpl_vector* fluximgcol = NULL;
2957 cpl_vector* errimgcol = NULL;
2958 cpl_boolean got_ancillary_data = CPL_FALSE;
2959 cpl_size assoc_key_offset = 1;
2960 int lamnlin = -1;
2961 double lamrms = NAN;
2962 double specerr = NAN;
2963 double specsye = NAN;
2964 int obsid = -1;
2965 const char *dateobs = NULL;
2966
2967 cpl_error_ensure(flux_filename != NULL && err_filename != NULL
2968 && allframes != NULL && parlist != NULL
2969 && recipe_id != NULL, CPL_ERROR_NULL_INPUT, goto cleanup,
2970 "NULL input parameters.");
2971
2972 error |= cpl_propertylist_append_string(extrakeys, GIALIAS_PROCATG,
2973 GIALIAS_PROCATG_RBNSPEC_IDP);
2974 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_PROCATG,
2975 GIALIAS_PROCATG_COMMENT);
2976 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2977 "Could not set keyword '%s'.", GIALIAS_PROCATG);
2978
2979 /* Load the input flux and error data, including FITS header keywords. */
2980 errorcode = giraffe_image_load(fluximage, flux_filename, 0);
2981 cpl_error_ensure(errorcode == 0, cpl_error_get_code(), goto cleanup,
2982 "Could not load image data in primary HDU from '%s'.",
2983 flux_filename);
2984 errorcode = giraffe_image_load(errimage, err_filename, 0);
2985 cpl_error_ensure(errorcode == 0, cpl_error_get_code(), goto cleanup,
2986 "Could not load image data in primary HDU from '%s'.",
2987 err_filename);
2988
2989 giraffe_error_push();
2990 fibertable = giraffe_fiberlist_load(flux_filename, 1, GIALIAS_FIBER_SETUP);
2991 if (fibertable == NULL) {
2992 fibertable = giraffe_fiberlist_load(err_filename, 1,
2993 GIALIAS_FIBER_SETUP);
2994 fibertable_name = err_filename;
2995 } else {
2996 fibertable_name = flux_filename;
2997 }
2998 cpl_error_ensure(fibertable != NULL, CPL_ERROR_DATA_NOT_FOUND, goto cleanup,
2999 "Could not load the %s table from either '%s' or '%s'.",
3000 GIALIAS_FIBER_SETUP, flux_filename, err_filename);
3001 giraffe_error_pop();
3002
3003 /* Check that the image sizes are the same. */
3004 nx = cpl_image_get_size_x(giraffe_image_get(fluximage));
3005 ny = cpl_image_get_size_y(giraffe_image_get(fluximage));
3006 cpl_error_ensure(cpl_image_get_size_x(giraffe_image_get(errimage)) == nx
3007 && cpl_image_get_size_y(giraffe_image_get(errimage)) == ny,
3008 CPL_ERROR_INCOMPATIBLE_INPUT, goto cleanup,
3009 "The images in files '%s' and '%s' are not the same size.",
3010 flux_filename, err_filename);
3011
3012 /* Construct the used frame list from the existing list of all frames.
3013 * The frames to be included as the used frames are RAW and CALIB. */
3014 usedframes = cpl_frameset_new();
3015 rawframes = cpl_frameset_new();
3016 iterator = cpl_frameset_iterator_new(allframes);
3017 do {
3018 const cpl_frame* frame = cpl_frameset_iterator_get_const(iterator);
3019 if (frame != NULL) {
3020 switch (cpl_frame_get_group(frame)) {
3021 case CPL_FRAME_GROUP_RAW:
3022 /* Mark the first RAW frame from which to inherit keywords. */
3023 if (inherit == NULL) inherit = frame;
3024 error |= cpl_frameset_insert(rawframes,
3025 cpl_frame_duplicate(frame));
3026 error |= cpl_frameset_insert(usedframes,
3027 cpl_frame_duplicate(frame));
3028 break;
3029 case CPL_FRAME_GROUP_CALIB:
3030 error |= cpl_frameset_insert(usedframes,
3031 cpl_frame_duplicate(frame));
3032 break;
3033 default: /* Ignore all other groups */
3034 break;
3035 }
3036 }
3037 prestate = cpl_errorstate_get();
3038 error |= cpl_frameset_iterator_advance(iterator, 1);
3039 if (error == CPL_ERROR_ACCESS_OUT_OF_RANGE) {
3040 cpl_errorstate_set(prestate);
3041 break;
3042 } else if (error != CPL_ERROR_NONE) {
3043 goto cleanup;
3044 }
3045 } while (1);
3046
3047 cpl_error_ensure(inherit != NULL, CPL_ERROR_DATA_NOT_FOUND, goto cleanup,
3048 "No raw input frames found.");
3049
3050 /* Fetch the EXPTIME and MJD-OBS keywords from the product file. */
3051 props = giraffe_image_get_properties(fluximage);
3052 prestate = cpl_errorstate_get();
3053 exptime = cpl_propertylist_get_double(props, GIALIAS_EXPTIME);
3054 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3055 goto cleanup, "Could not find keyword '%s' in '%s'.",
3056 GIALIAS_EXPTIME, flux_filename);
3057 mjdobs = cpl_propertylist_get_double(props, GIALIAS_MJDOBS);
3058 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3059 goto cleanup, "Could not find keyword '%s' in '%s'.",
3060 GIALIAS_MJDOBS, flux_filename);
3061
3062 mjdend = mjdobs + exptime / 86400.;
3063
3064 /* Fetch the DATE-OBS and ESO OBS ID keywords from the product file. */
3065
3066 dateobs = cpl_propertylist_get_string(props, GIALIAS_DATEOBS);
3067 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3068 goto cleanup, "Could not find keyword '%s' in '%s'.",
3069 GIALIAS_DATEOBS, flux_filename);
3070
3071 obsid = cpl_propertylist_get_int(props, GIALIAS_OBSID);
3072 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3073 goto cleanup, "Could not find keyword '%s' in '%s'.",
3074 GIALIAS_OBSID, flux_filename);
3075
3076
3077 /* Calculate the min/max wavelength values. */
3078 crpix2 = cpl_propertylist_get_double(props, GIALIAS_CRPIX2);
3079 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3080 goto cleanup, "Could not find keyword '%s' in '%s'.",
3081 GIALIAS_CRPIX2, flux_filename);
3082 crval2 = cpl_propertylist_get_double(props, GIALIAS_CRVAL2);
3083 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3084 goto cleanup, "Could not find keyword '%s' in '%s'.",
3085 GIALIAS_CRVAL2, flux_filename);
3086 cdelt2 = cpl_propertylist_get_double(props, GIALIAS_CDELT2);
3087 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3088 goto cleanup, "Could not find keyword '%s' in '%s'.",
3089 GIALIAS_CDELT2, flux_filename);
3090 cunit2 = cpl_propertylist_get_string(props, GIALIAS_CUNIT2);
3091 cpl_error_ensure(cunit2 != NULL, cpl_error_get_code(),
3092 goto cleanup, "Could not find keyword '%s' in '%s'.",
3093 GIALIAS_CUNIT2, flux_filename);
3094
3095 if (strcmp(cunit2, "nm") == 0) {
3096 wavelmin = (1.0 - crpix2) * cdelt2 + crval2;
3097 wavelmax = ((double)ny - crpix2) * cdelt2 + crval2;
3098 if (wavelmax < wavelmin) {
3099 double tmp = wavelmin;
3100 wavelmin = wavelmax;
3101 wavelmax = tmp;
3102 }
3103 specbin = fabs(cdelt2);
3104 } else {
3105 cpl_msg_warning(cpl_func, "Do not know how to handle keyword %s = '%s'."
3106 " Will not set WAVELMIN, WAVELMAX or SPEC_BIN.",
3107 GIALIAS_CUNIT2, cunit2);
3108 }
3109
3110 if (cpl_propertylist_has(props, GIALIAS_SETUPNAME)) {
3111 expmode = cpl_propertylist_get_string(props, GIALIAS_SETUPNAME);
3112 cpl_error_ensure(expmode != NULL, cpl_error_get_code(), goto cleanup,
3113 "Could not fetch the keyword '%s' from '%s'.",
3114 GIALIAS_SETUPNAME, flux_filename);
3115 } else if (cpl_propertylist_has(props, GIALIAS_GRATNAME)) {
3116 const char* name = cpl_propertylist_get_string(props, GIALIAS_GRATNAME);
3117 cpl_error_ensure(name != NULL, cpl_error_get_code(), goto cleanup,
3118 "Could not fetch the keyword '%s' from '%s'.",
3119 GIALIAS_GRATNAME, flux_filename);
3120 double wlen = cpl_propertylist_get_double(props, GIALIAS_GRATWLEN);
3121 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3122 cpl_error_get_code(), goto cleanup,
3123 "Could not find keyword '%s' in '%s'.",
3124 GIALIAS_GRATWLEN, flux_filename);
3125 strbuf[0] = name[0];
3126 char* numstr = cpl_sprintf("%.1f", wlen);
3127 strncpy(strbuf+1, numstr, sizeof(strbuf)-1);
3128 cpl_free(numstr);
3129 strbuf[sizeof(strbuf)-1] = '\0'; /* Ensure we have a NULL terminator. */
3130 expmode = strbuf;
3131 } else {
3132 cpl_error_set_message(cpl_func, CPL_ERROR_DATA_NOT_FOUND,
3133 "Neither '%s' nor '%s' and '%s' keywords were found in the"
3134 " file '%s'.", GIALIAS_SETUPNAME, GIALIAS_GRATNAME,
3135 GIALIAS_GRATWLEN, flux_filename);
3136 goto cleanup;
3137 }
3138
3139 specres = _giraffe_lookup_specres(expmode);
3140 if (isnan(specres)) {
3141 cpl_error_set_message(cpl_func, CPL_ERROR_ILLEGAL_INPUT,
3142 "The exposure mode '%s' is invalid or an unknown value."
3143 " Could not lookup the spectral resolution for 'SPEC_RES'.",
3144 expmode);
3145 goto cleanup;
3146 }
3147
3148 /* Add the FILTER keyword as OFILTER to the extra keywords list if it
3149 * exists. The FILTER keyword itself will be deleted. */
3150 if (cpl_propertylist_has(props, "FILTER")) {
3151 prestate = cpl_errorstate_get();
3152 cpl_propertylist_copy_property(extrakeys, props, "FILTER");
3153 cpl_property* prop = cpl_propertylist_get_property(extrakeys, "FILTER");
3154 cpl_property_set_name(prop, "OFILTER");
3155 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3156 cpl_error_get_code(), goto cleanup,
3157 "Could not rename the 'FILTER' keyword.");
3158 }
3159
3160 /* Write the ancillary data file if any ancillary data is available. */
3161 prestate = cpl_errorstate_get();
3162 got_ancillary_data = _giraffe_ancillary_data_available(flux_filename,
3163 fibertable);
3164 if (! cpl_errorstate_is_equal(prestate)) goto cleanup;
3165 if (got_ancillary_data) {
3166 error = _giraffe_make_ancillary_file(allframes, ancillary_filename,
3167 flux_filename, fluximage,
3168 fibertable);
3169 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3170 "Failed to write the ancillary file '%s'.",
3171 ancillary_filename);
3172 }
3173
3174 /* Create a new spectrum object and setup header keywords. */
3175 spectrum = irplib_sdp_spectrum_new();
3176 error = CPL_ERROR_NONE;
3177 error |= irplib_sdp_spectrum_set_origin(spectrum, GIALIAS_ORIGIN_VALUE);
3178 error |= irplib_sdp_spectrum_set_prodlvl(spectrum, GIALIAS_PRODLVL_VALUE);
3179 error |= irplib_sdp_spectrum_copy_dispelem(spectrum,
3180 props, GIALIAS_GRATNAME);
3181 error |= irplib_sdp_spectrum_set_specsys(spectrum, GIALIAS_SPECSYS_VALUE);
3182 error |= irplib_sdp_spectrum_set_extobj(spectrum, GIALIAS_EXT_OBJ_VALUE);
3183 /* The OBJECT, RA and DEC keywords we fill now with dummy values to maintain
3184 * the order of keywords. The actual values are set later. */
3185 error |= irplib_sdp_spectrum_set_object(spectrum, "");
3186 error |= irplib_sdp_spectrum_set_ra(spectrum, 0.0);
3187 error |= irplib_sdp_spectrum_set_dec(spectrum, 0.0);
3188 error |= irplib_sdp_spectrum_copy_exptime(spectrum, props, GIALIAS_EXPTIME);
3189 error |= irplib_sdp_spectrum_copy_texptime(spectrum,
3190 props, GIALIAS_EXPTIME);
3191 error |= irplib_sdp_spectrum_copy_mjdobs(spectrum, props, GIALIAS_MJDOBS);
3192 error |= irplib_sdp_spectrum_set_mjdend(spectrum, mjdend);
3193 if (cpl_propertylist_has(props, GIALIAS_TIMESYS)) {
3194 error |= irplib_sdp_spectrum_copy_timesys(spectrum,
3195 props, GIALIAS_TIMESYS);
3196 }
3197 error |= irplib_sdp_spectrum_copy_progid(spectrum, props, GIALIAS_PROGID);
3198 error |= irplib_sdp_spectrum_copy_obid(spectrum, 1, props, GIALIAS_OBSID);
3199 error |= irplib_sdp_spectrum_set_mepoch(spectrum, GIALIAS_M_EPOCH_VALUE);
3200 error |= irplib_sdp_spectrum_append_prov(spectrum, 1, rawframes);
3201 error |= irplib_sdp_spectrum_copy_procsoft(spectrum,
3202 props, GIALIAS_PROPIPEID);
3203 error |= irplib_sdp_spectrum_copy_obstech(spectrum, props, GIALIAS_PROTECH);
3204 error |= irplib_sdp_spectrum_set_prodcatg(spectrum, GIALIAS_PRODCATG_VALUE);
3205 error |= irplib_sdp_spectrum_set_fluxcal(spectrum, GIALIAS_FLUXCAL_VALUE);
3206 error |= irplib_sdp_spectrum_set_contnorm(spectrum, GIALIAS_CONTNORM_VALUE);
3207 /* Set dummy values for WAVELMIN, WAVELMAX and SPEC_BIN to keep the order
3208 * of the keywords. Will fill these in later with actual Heliocentric
3209 * corrected values. */
3210 error |= irplib_sdp_spectrum_set_wavelmin(spectrum, 0.0);
3211 error |= irplib_sdp_spectrum_set_wavelmax(spectrum, 0.0);
3212 error |= irplib_sdp_spectrum_set_specbin(spectrum, 0.0);
3213 error |= irplib_sdp_spectrum_set_totflux(spectrum, GIALIAS_TOTFLUX_VALUE);
3214 error |= irplib_sdp_spectrum_set_fluxerr(spectrum, GIALIAS_FLUXERR_VALUE);
3215 error |= irplib_sdp_spectrum_set_ncombine(spectrum,
3216 cpl_frameset_get_size(rawframes));
3217 error |= irplib_sdp_spectrum_set_referenc(spectrum, GIALIAS_REFERENC);
3218
3219 /* Set dummy value for SNR to maintain keyword ordering. Filled later. */
3220 error |= irplib_sdp_spectrum_set_snr(spectrum, 0.0);
3221
3222 /* Copy LAMNLIN if available from flux image else try look it up. */
3223 if (cpl_propertylist_has(props, GIALIAS_LAMNLIN)) {
3224 error |= irplib_sdp_spectrum_copy_lamnlin(spectrum, props,
3225 GIALIAS_LAMNLIN);
3226 lamnlin = irplib_sdp_spectrum_get_lamnlin(spectrum);
3227 } else {
3228 lamnlin = _giraffe_lookup_lamnlin(expmode);
3229 if (lamnlin != -1) {
3230 error |= irplib_sdp_spectrum_set_lamnlin(spectrum, lamnlin);
3231 }
3232 }
3233
3234 /* Copy LAMRMS if available from flux image else try look it up.
3235 * Note: we are going to have to correct this value later and fill it in
3236 * again for each spectrum. */
3237 if (cpl_propertylist_has(props, GIALIAS_LAMRMS)) {
3238 error |= irplib_sdp_spectrum_copy_lamrms(spectrum, props,
3239 GIALIAS_LAMRMS);
3240 lamrms = irplib_sdp_spectrum_get_lamrms(spectrum);
3241 } else {
3242 lamrms = _giraffe_lookup_lamrms(expmode);
3243 if (! isnan(lamrms)) {
3244 error |= irplib_sdp_spectrum_set_lamrms(spectrum, lamrms);
3245 }
3246 }
3247
3248 /* Copy SPEC_ERR if available from the flux image, else estimate it as:
3249 * if CRDER1 is available then
3250 * SPEC_ERR = CRDER1 / sqrt(LAMNLIN)
3251 * else
3252 * SPEC_ERR = LAMRMS / sqrt(LAMNLIN)
3253 * end
3254 *
3255 * Note: we are going to have to correct this value later and fill it in
3256 * again for each spectrum.
3257 */
3258 if (cpl_propertylist_has(props, GIALIAS_SPEC_ERR)) {
3259 error |= irplib_sdp_spectrum_copy_specerr(spectrum, props,
3260 GIALIAS_SPEC_ERR);
3261 specerr = irplib_sdp_spectrum_get_specerr(spectrum);
3262 } else if (lamnlin > 0) {
3263 if (cpl_propertylist_has(props, GIALIAS_CRDER1)) {
3264 prestate = cpl_errorstate_get();
3265 double crder1 = cpl_propertylist_get_double(props, GIALIAS_CRDER1);
3266 if (cpl_errorstate_is_equal(prestate) && crder1 > 0) {
3267 specerr = crder1 / sqrt(lamnlin);
3268 } else {
3269 error = cpl_error_get_code();
3270 }
3271 } else if (! isnan(lamrms)) {
3272 specerr = lamrms / sqrt(lamnlin);
3273 }
3274 if (! isnan(specerr)) {
3275 error |= irplib_sdp_spectrum_set_specerr(spectrum, specerr);
3276 }
3277 }
3278
3279 /* Copy SPEC_SYE if available from the flux image, else estimate it as:
3280 * 0.002 nm
3281 */
3282 if (cpl_propertylist_has(props, GIALIAS_SPEC_SYE)) {
3283 error |= irplib_sdp_spectrum_copy_specsye(spectrum, props,
3284 GIALIAS_SPEC_SYE);
3285 specsye = irplib_sdp_spectrum_get_specsye(spectrum);
3286 } else {
3287 /* Don't set the local specsye variable so that it does not get
3288 * corrected later. We want it to always be 0.002 nm. Just set the
3289 * keyword in the spectrum object directly. */
3290 error |= irplib_sdp_spectrum_set_specsye(spectrum, 0.002);
3291 }
3292
3293 error |= irplib_sdp_spectrum_set_specres(spectrum, specres);
3294 error |= irplib_sdp_spectrum_copy_gain(spectrum, props, GIALIAS_CONAD);
3295 error |= irplib_sdp_spectrum_copy_detron(spectrum, props, GIALIAS_RON);
3296 if (got_ancillary_data) {
3297 /* This assumes ancillary_filename points to a fits file
3298 * this is currently always the case, otherwise the keywords
3299 * assoc and assom must also be added. */
3300 error |= irplib_sdp_spectrum_set_asson(spectrum, 1, ancillary_filename);
3301 assoc_key_offset = 2;
3302 }
3303 for (i = assoc_key_offset; i < nassoc_keys + assoc_key_offset; ++i) {
3304 /* Add extra dummy association keywords if requested. */
3305 error |= irplib_sdp_spectrum_set_asson(spectrum, i, "");
3306 error |= irplib_sdp_spectrum_set_assoc(spectrum, i, "");
3307 error |= irplib_sdp_spectrum_set_assom(spectrum, i, "");
3308 }
3309
3310 error |= irplib_sdp_spectrum_set_voclass(spectrum, GIALIAS_VOCLASS_VALUE);
3311 error |= irplib_sdp_spectrum_set_vopub(spectrum, GIALIAS_VOPUB_VALUE);
3312 error |= irplib_sdp_spectrum_set_title(spectrum, ""); /* Set dummy value */
3313 error |= cpl_propertylist_append_double(tablekeys, GIALIAS_APERTURE,
3314 GIALIAS_APERTURE_VALUE);
3315 error |= cpl_propertylist_set_comment(tablekeys, GIALIAS_APERTURE,
3316 GIALIAS_APERTURE_COMMENT);
3317 /*
3318 * Normally: telapse = (mjdend - mjdobs) * 86400.
3319 * However, doing this calculation directly leads to rounding errors that
3320 * can cause the invalid condition TELAPSE < EXPTIME. Since we have:
3321 * mjdend = mjdobs + exptime / 86400.
3322 * we can simplify the above to be: telapse = exptime
3323 * which will always satisfy the condition TELAPSE >= EXPTIME.
3324 */
3325 error |= irplib_sdp_spectrum_set_telapse(spectrum, exptime);
3326 error |= irplib_sdp_spectrum_set_tmid(spectrum, (mjdobs + mjdend) * 0.5);
3327 /* Set dummy values for the SPEC_VAL, SPEC_BW, TDMIN and TDMAX values to
3328 * keep the order of the keywords on the header. Will fill these in later
3329 * with Heliocentric corrected values. */
3330 error |= irplib_sdp_spectrum_set_specval(spectrum, 0.0);
3331 error |= irplib_sdp_spectrum_set_specbw(spectrum, 0.0);
3332 error |= irplib_sdp_spectrum_set_nelem(spectrum, ny);
3333 error |= irplib_sdp_spectrum_set_tdmin(spectrum, 0.0);
3334 error |= irplib_sdp_spectrum_set_tdmax(spectrum, 0.0);
3335
3336 /* Add the keyword FPS */
3337 error |= cpl_propertylist_append_int(extrakeys, GIALIAS_FPS, -1);
3338 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_FPS,
3339 GIALIAS_FPS_COMMENT);
3340
3341 /* Add dummy [G,H,B]CORR keywords to be updated from the fiber table. */
3342 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_GEOCORR, NAN);
3343 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_GEOCORR,
3344 GIALIAS_GEOCORR_COMMENT);
3345 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_HELICORR, NAN);
3346 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_HELICORR,
3347 GIALIAS_HELICORR_COMMENT);
3348 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_BARYCORR, NAN);
3349 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_BARYCORR,
3350 GIALIAS_BARYCORR_COMMENT);
3351
3352 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3353 "Could not setup the common SDP spectrum keywords.");
3354
3355 for (int qci = 0; qci < (int)(sizeof(sciqcpar) / sizeof(sciqcpar[0])); qci++) {
3356 if (cpl_propertylist_has(props, sciqcpar[qci])) {
3357 cpl_propertylist_copy_property(extrakeys, props, sciqcpar[qci]);
3358 }
3359 }
3360
3361 /* Figure out the data type required for the WAVE column to preserve the
3362 * precision of the data values. */
3363 wavecoltype = _giraffe_calc_wave_type(crval2, crpix2, cdelt2, ny);
3364
3365 /* Calculate the reference wavelength values (before corrections). */
3366 refwavearray = cpl_array_new(ny, CPL_TYPE_DOUBLE);
3367 data_double = cpl_array_get_data_double(refwavearray);
3368 assert(data_double != NULL);
3369 for (i = 1; i <= ny; ++i) {
3370 data_double[i-1] = (i-crpix2) * cdelt2 + crval2;
3371 }
3372 data_double = NULL;
3373
3374 /* Try setup the SDP table columns. */
3375 error |= irplib_sdp_spectrum_add_column(
3376 spectrum, GIALIAS_COLUMN_WAVE, wavecoltype,
3377 GIALIAS_COLUMN_WAVE_UNIT, NULL, GIALIAS_COLUMN_WAVE_TUTYP,
3378 GIALIAS_COLUMN_WAVE_TUCD, NULL);
3379
3380 /* Replace default keyword comment of the just created column */
3381 error |= irplib_sdp_spectrum_replace_column_comment(
3382 spectrum, GIALIAS_COLUMN_WAVE, "TUCD", "Air wavelength");
3383
3384 error |= irplib_sdp_spectrum_set_column_tcomm(
3385 spectrum, GIALIAS_COLUMN_WAVE, GIALIAS_COLUMN_WAVE_TCOMM);
3386 error |= irplib_sdp_spectrum_add_column(
3387 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, CPL_TYPE_DOUBLE,
3388 GIALIAS_COLUMN_FLUX_REDUCED_UNIT, NULL,
3389 GIALIAS_COLUMN_FLUX_REDUCED_TUTYP,
3390 GIALIAS_COLUMN_FLUX_REDUCED_TUCD, NULL);
3391 error |= irplib_sdp_spectrum_set_column_tcomm(
3392 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, "");
3393 error |= irplib_sdp_spectrum_add_column(
3394 spectrum, GIALIAS_COLUMN_ERR_REDUCED, CPL_TYPE_DOUBLE,
3395 GIALIAS_COLUMN_ERR_REDUCED_UNIT, NULL,
3396 GIALIAS_COLUMN_ERR_REDUCED_TUTYP,
3397 GIALIAS_COLUMN_ERR_REDUCED_TUCD, NULL);
3398 error |= irplib_sdp_spectrum_set_column_tcomm(
3399 spectrum, GIALIAS_COLUMN_ERR_REDUCED, "");
3400 error |= irplib_sdp_spectrum_add_column(
3401 spectrum, GIALIAS_COLUMN_SNR, CPL_TYPE_DOUBLE,
3402 GIALIAS_COLUMN_SNR_UNIT, NULL, GIALIAS_COLUMN_SNR_TUTYP,
3403 GIALIAS_COLUMN_SNR_TUCD, NULL);
3404 error |= irplib_sdp_spectrum_set_column_tcomm(
3405 spectrum, GIALIAS_COLUMN_SNR, GIALIAS_COLUMN_SNR_TCOMM);
3406 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3407 "Could not setup the SDP spectrum columns.");
3408
3409 indices = cpl_table_get_data_int_const(giraffe_table_get(fibertable),
3410 GIALIAS_COLUMN_INDEX);
3411 fps = cpl_table_get_data_int_const(giraffe_table_get(fibertable),
3412 GIALIAS_FPS);
3413 objects = cpl_table_get_data_string_const(giraffe_table_get(fibertable),
3414 GIALIAS_COLUMN_OBJECT);
3415 spectypes = cpl_table_get_data_string_const(giraffe_table_get(fibertable),
3416 GIALIAS_COLUMN_TYPE);
3417 ras = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3418 GIALIAS_COLUMN_RA);
3419 decs = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3420 GIALIAS_COLUMN_DEC);
3421 gcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3422 GIALIAS_COLUMN_GCORR);
3423 hcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3424 GIALIAS_COLUMN_HCORR);
3425 bcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3426 GIALIAS_COLUMN_BCORR);
3427 cpl_error_ensure(indices != NULL && fps != NULL && objects != NULL
3428 && spectypes != NULL && ras != NULL && decs != NULL
3429 && gcorr != NULL && hcorr != NULL && bcorr != NULL,
3430 cpl_error_get_code(), goto cleanup,
3431 "Could not fetch data from the fiber setup table in '%s'.",
3432 fibertable_name);
3433
3434 formatstr = _giraffe_calc_format_string(
3435 cpl_table_get_nrow(giraffe_table_get(fibertable)));
3436
3437 cpl_errorstate tempes = cpl_errorstate_get();
3438
3439 cpl_size maxx = -1;
3440 cpl_size maxy = -1;
3441 cpl_image * maxim = cpl_image_collapse_create(giraffe_image_get(fluximage),0);
3442 cpl_image_get_maxpos(maxim, &maxx, &maxy);
3443
3444 cpl_image_delete(maxim);
3445
3446 cpl_errorstate_set(tempes);
3447
3448 data_float = cpl_malloc(ny * sizeof(float));
3449 data_double = cpl_malloc(ny * sizeof(double));
3450
3451 /* Write the individual spectrum files: */
3452 filecount = 0;
3453 for (i = 0; i < cpl_table_get_nrow(giraffe_table_get(fibertable)); ++i) {
3454 const double* wave_data;
3455 double* flux_data;
3456 double* err_data;
3457 cpl_size j;
3458 double snr = 0.0;
3459 /* Keywords to remove: */
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"
3462 "|BLANK|FILTER)$";
3463 cpl_size specindex = indices[i];
3464 double vela, velb, beta;
3465 double correction_factor = 1.0;
3466
3467 /* Skip non-science spectra. */
3468 if (strcmp(spectypes[i], "M") != 0) continue;
3469
3470 filename = cpl_sprintf(formatstr, ++filecount);
3471
3472 /* Calculate the Heliocentric correction factor to apply.
3473 * The gcorr and hcorr values are in km/s, so must be converted to m/s.
3474 */
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));
3485
3486 /* Calculate and set corrected wavelength array, remembering to cast
3487 * to the appropriate type. */
3488 wave_data = cpl_array_get_data_double_const(refwavearray);
3489 if (wavecoltype == CPL_TYPE_FLOAT) {
3490 for (j = 0; j < ny; ++j) {
3491 data_float[j] = wave_data[j] * correction_factor;
3492 }
3493 array = cpl_array_wrap_float(data_float, ny);
3494 } else {
3495 for (j = 0; j < ny; ++j) {
3496 data_double[j] = wave_data[j] * correction_factor;
3497 }
3498 array = cpl_array_wrap_double(data_double, ny);
3499 }
3500 error |= irplib_sdp_spectrum_set_column_data(
3501 spectrum, GIALIAS_COLUMN_WAVE, array);
3502 cpl_array_unwrap(array);
3503 array = NULL;
3504
3505 fluximgcol = cpl_vector_new_from_image_column(
3506 giraffe_image_get(fluximage), specindex);
3507 flux_data = cpl_vector_get_data(fluximgcol);
3508 cpl_error_ensure(flux_data != NULL, cpl_error_get_code(), goto cleanup,
3509 "Unable to extract data in column %"CPL_SIZE_FORMAT
3510 " from image in file '%s'.", specindex, flux_filename);
3511 array = cpl_array_wrap_double(flux_data, ny);
3512
3513 if(i==maxx - 1){
3514 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG, 'Y');
3515 }
3516 else{
3517 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG, 'N');
3518 }
3519
3520 double fluxmean = cpl_array_get_mean(array);
3521 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMEANRED, fluxmean);
3522 error |= irplib_sdp_spectrum_set_column_data(
3523 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, array);
3524 cpl_array_unwrap(array);
3525 array = NULL;
3526
3527 errimgcol = cpl_vector_new_from_image_column(
3528 giraffe_image_get(errimage), specindex);
3529 err_data = cpl_vector_get_data(errimgcol);
3530 cpl_error_ensure(err_data != NULL, cpl_error_get_code(), goto cleanup,
3531 "Unable to extract data in column %"CPL_SIZE_FORMAT
3532 " from image in file '%s'.", specindex, err_filename);
3533 array = cpl_array_wrap_double(err_data, ny);
3534 error |= irplib_sdp_spectrum_set_column_data(
3535 spectrum, GIALIAS_COLUMN_ERR_REDUCED, array);
3536 cpl_array_unwrap(array);
3537 array = NULL;
3538
3539 for (j = 0; j < ny; ++j) {
3540 data_double[j] = (err_data[j] != 0.0) ? flux_data[j] / err_data[j]
3541 : 0.0;
3542 }
3543 array = cpl_array_wrap_double(data_double, ny);
3544 snr = cpl_array_get_median(array);
3545 double snrmean = cpl_array_get_mean(array);
3546 cpl_propertylist_update_double(extrakeys, GIALIAS_QCSNR, snrmean);
3547 error |= irplib_sdp_spectrum_set_column_data(spectrum,
3548 GIALIAS_COLUMN_SNR, array);
3549 cpl_array_unwrap(array);
3550 array = NULL;
3551
3552 cpl_vector_delete(fluximgcol);
3553 fluximgcol = NULL;
3554 cpl_vector_delete(errimgcol);
3555 errimgcol = NULL;
3556
3557 double estmag = 0;
3558 if(cpl_table_has_column(giraffe_table_get(fibertable), "MAGNITUDE")){
3559 estmag = cpl_table_get_double(giraffe_table_get(fibertable), "MAGNITUDE", i, NULL);
3560 }
3561 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMAG, estmag);
3562
3563 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3564 "Could not setup the SDP spectrum columns for '%s'.",
3565 filename);
3566
3567 error |= irplib_sdp_spectrum_set_object(spectrum, objects[i]);
3568
3569 char * tmp_string;
3570
3571 tmp_string = cpl_sprintf("%s_%d_%s",
3572 objects[i],
3573 obsid,
3574 dateobs
3575 );
3576
3577 replace_spaces_with_underscores(tmp_string);
3578
3579 error |= irplib_sdp_spectrum_set_title(spectrum, tmp_string);
3580
3581 cpl_free(tmp_string);
3582
3583 error |= irplib_sdp_spectrum_set_ra(spectrum, ras[i]);
3584 error |= irplib_sdp_spectrum_set_dec(spectrum, decs[i]);
3585 error |= irplib_sdp_spectrum_set_snr(spectrum, snr);
3586 error |= irplib_sdp_spectrum_set_column_tcomm(
3587 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, flux_filename);
3588 error |= irplib_sdp_spectrum_set_column_tcomm(
3589 spectrum, GIALIAS_COLUMN_ERR_REDUCED, err_filename);
3590
3591 error |= cpl_propertylist_update_int(extrakeys, GIALIAS_FPS, fps[i]);
3592 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_GEOCORR,
3593 gcorr[i]);
3594 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_HELICORR,
3595 hcorr[i]);
3596 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_BARYCORR,
3597 bcorr[i]);
3598
3599 /* Set corrected values that depend on wavelengths. */
3600 error |= irplib_sdp_spectrum_set_wavelmin(spectrum,
3601 wavelmin * correction_factor);
3602 error |= irplib_sdp_spectrum_set_wavelmax(spectrum,
3603 wavelmax * correction_factor);
3604 error |= irplib_sdp_spectrum_set_specval(spectrum,
3605 (wavelmax + wavelmin) * 0.5 * correction_factor);
3606 error |= irplib_sdp_spectrum_set_specbw(spectrum,
3607 (wavelmax - wavelmin) * correction_factor);
3608 error |= irplib_sdp_spectrum_set_tdmin(spectrum,
3609 wavelmin * correction_factor);
3610 error |= irplib_sdp_spectrum_set_tdmax(spectrum,
3611 wavelmax * correction_factor);
3612 error |= irplib_sdp_spectrum_set_specbin(spectrum,
3613 specbin * correction_factor);
3614 if (! isnan(lamrms)) {
3615 error |= irplib_sdp_spectrum_set_lamrms(spectrum,
3616 lamrms * correction_factor);
3617 }
3618 if (! isnan(specerr)) {
3619 error |= irplib_sdp_spectrum_set_specerr(spectrum,
3620 specerr * correction_factor);
3621 }
3622 if (! isnan(specsye)) {
3623 error |= irplib_sdp_spectrum_set_specsye(spectrum,
3624 specsye * correction_factor);
3625 }
3626
3627 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3628 "Could not setup the SDP spectrum keywords for '%s'.",
3629 filename);
3630
3631 error |= irplib_dfs_save_spectrum(allframes, NULL, parlist, usedframes,
3632 inherit, spectrum, recipe_id,
3633 extrakeys, tablekeys, remregexp,
3634 pipe_id, dict_id, filename);
3635 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3636 "Failed to save SDP spectrum %"CPL_SIZE_FORMAT
3637 " to file '%s'.", specindex, filename);
3638
3639 error |= irplib_fits_update_checksums(filename);
3640 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3641 "Failed to save update checksums for file '%s'.",
3642 filename);
3643 cpl_free(filename);
3644 filename = NULL;
3645 }
3646
3647 if (filecount == 0) {
3648 cpl_msg_warning(cpl_func, "No science spectra found in '%s'."
3649 " No SDP spectra created.", flux_filename);
3650 }
3651
3652 result_code = 0; /* Indicate success. */
3653
3654cleanup:
3655 /* Cleanup objects and memory. Note: the delete functions already check for
3656 * NULL pointers. */
3657 cpl_vector_delete(fluximgcol);
3658 cpl_vector_delete(errimgcol);
3659 cpl_array_unwrap(array);
3660 cpl_array_delete(refwavearray);
3661 cpl_free(data_float);
3662 cpl_free(data_double);
3663 cpl_free(filename);
3664 cpl_free(formatstr);
3665 cpl_frameset_delete(usedframes);
3666 cpl_frameset_delete(rawframes);
3667 cpl_frameset_iterator_delete(iterator);
3668 cpl_free(pipe_id);
3669 cpl_propertylist_delete(tablekeys);
3670 cpl_propertylist_delete(extrakeys);
3671 giraffe_image_delete(fluximage);
3672 giraffe_image_delete(errimage);
3673 giraffe_table_delete(fibertable);
3674 irplib_sdp_spectrum_delete(spectrum);
3675 return result_code;
3676}
giraffe_add_rvcorrection
cxint giraffe_add_rvcorrection(GiTable *fibers, const GiImage *spectra)
Add the barycentric and heliocentric corrections to the given fiber setup.
Definition: giastrometry.c:69
giraffe_bias_config_create
GiBiasConfig * giraffe_bias_config_create(cpl_parameterlist *list)
Creates a setup structure for a bias removal task.
Definition: gibias.c:3436
giraffe_bias_config_add
void giraffe_bias_config_add(cpl_parameterlist *list)
Adds parameters for the bias removal.
Definition: gibias.c:3595
giraffe_bias_remove
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.
Definition: gibias.c:3104
giraffe_bias_config_destroy
void giraffe_bias_config_destroy(GiBiasConfig *config)
Destroys a bias removal setup structure.
Definition: gibias.c:3567
giraffe_subtract_dark
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.
Definition: gidark.c:480
giraffe_extract_config_add
void giraffe_extract_config_add(cpl_parameterlist *list)
Adds parameters for the spectrum extraction.
Definition: giextract.c:3509
giraffe_extract_spectra
cxint giraffe_extract_spectra(GiExtraction *result, GiImage *image, GiTable *fibers, GiLocalization *sloc, GiImage *bpixel, GiImage *slight, GiExtractConfig *config)
Extracts the spectra from a preprocessed frame.
Definition: giextract.c:2480
giraffe_extract_config_create
GiExtractConfig * giraffe_extract_config_create(cpl_parameterlist *list)
Creates a setup structure for the spectrum extraction.
Definition: giextract.c:3405
giraffe_extract_config_destroy
void giraffe_extract_config_destroy(GiExtractConfig *config)
Destroys a spectrum extraction setup structure.
Definition: giextract.c:3479
giraffe_fibers_setup
GiTable * giraffe_fibers_setup(const cpl_frame *frame, const cpl_frame *reference)
Setup a fiber list.
Definition: gifibers.c:218
giraffe_fiberlist_load
GiTable * giraffe_fiberlist_load(const cxchar *filename, cxint dataset, const cxchar *tag)
Load a fiber table from a file.
Definition: gifiberutils.c:754
giraffe_fiberlist_compare
cxint giraffe_fiberlist_compare(const GiTable *fibers, const GiTable *reference)
Compare two fiber lists.
Definition: gifiberutils.c:952
giraffe_fiberlist_attach
cxint giraffe_fiberlist_attach(cpl_frame *frame, GiTable *fibers)
Attach a fiber table to a frame.
Definition: gifiberutils.c:884
giraffe_flat_config_create
GiFlatConfig * giraffe_flat_config_create(cpl_parameterlist *list)
Creates a setup structure for the flat field correction.
Definition: giflat.c:302
giraffe_flat_config_destroy
void giraffe_flat_config_destroy(GiFlatConfig *config)
Destroys a flat field setup structure.
Definition: giflat.c:353
giraffe_flat_config_add
void giraffe_flat_config_add(cpl_parameterlist *list)
Adds parameters for the flat field correction.
Definition: giflat.c:376
giraffe_flat_apply
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.
Definition: giflat.c:238
giraffe_fov_config_create
GiFieldOfViewConfig * giraffe_fov_config_create(cpl_parameterlist *list)
Creates a setup structure for the field of view reconstruction.
Definition: gifov.c:2002
giraffe_fov_config_destroy
void giraffe_fov_config_destroy(GiFieldOfViewConfig *config)
Destroys a field of view setup structure.
Definition: gifov.c:2057
giraffe_fov_new
GiFieldOfView * giraffe_fov_new(void)
Create an empty container for the results of the field of view reconstruction.
Definition: gifov.c:1383
giraffe_fov_save_cubes_eso3d
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.
Definition: gifov.c:1663
giraffe_fov_delete
void giraffe_fov_delete(GiFieldOfView *self)
Deallocate a field of view object and its contents.
Definition: gifov.c:1484
giraffe_fov_build
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.
Definition: gifov.c:418
giraffe_fov_save_cubes
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.
Definition: gifov.c:1520
giraffe_fov_config_add
void giraffe_fov_config_add(cpl_parameterlist *list)
Adds parameters for the image and data cube construction.
Definition: gifov.c:2079
giraffe_frame_create
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.
Definition: giframe.c:239
giraffe_frame_create_image
cpl_frame * giraffe_frame_create_image(GiImage *image, const cxchar *tag, cpl_frame_level level, cxbool save, cxbool update)
Create an image product frame.
Definition: giframe.c:395
giraffe_get_slitgeometry
cpl_frame * giraffe_get_slitgeometry(const cpl_frameset *set)
Get the slit geometry frame from a frame set.
Definition: giframe.c:786
giraffe_image_get
cpl_image * giraffe_image_get(const GiImage *self)
Gets the image data.
Definition: giimage.c:218
giraffe_image_get_properties
cpl_propertylist * giraffe_image_get_properties(const GiImage *self)
Get the properties of an image.
Definition: giimage.c:282
giraffe_image_delete
void giraffe_image_delete(GiImage *self)
Destroys an image.
Definition: giimage.c:181
giraffe_image_create
GiImage * giraffe_image_create(cpl_type type, cxint nx, cxint ny)
Creates an image container of a given type.
Definition: giimage.c:95
giraffe_image_add_info
cxint giraffe_image_add_info(GiImage *image, const GiRecipeInfo *info, const cpl_frameset *set)
Add additional frame information to an image.
Definition: giimage.c:773
giraffe_image_save
cxint giraffe_image_save(GiImage *self, const cxchar *filename)
Write a Giraffe image to a file.
Definition: giimage.c:570
giraffe_image_new
GiImage * giraffe_image_new(cpl_type type)
Creates an empty image container.
Definition: giimage.c:65
giraffe_image_set_properties
cxint giraffe_image_set_properties(GiImage *self, cpl_propertylist *properties)
Attaches a property list to an image.
Definition: giimage.c:312
giraffe_image_load
cxint giraffe_image_load(GiImage *self, const cxchar *filename, cxint position)
Gets image data and properties from a file.
Definition: giimage.c:536
giraffe_rebin_config_destroy
void giraffe_rebin_config_destroy(GiRebinConfig *config)
Destroys a spectrum extraction setup structure.
Definition: girebinning.c:4926
giraffe_rebin_spectra
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.
Definition: girebinning.c:4052
giraffe_rebin_config_create
GiRebinConfig * giraffe_rebin_config_create(cpl_parameterlist *list)
Creates a setup structure for the rebinning.
Definition: girebinning.c:4826
giraffe_rebinning_new
GiRebinning * giraffe_rebinning_new(void)
Create an empty rebinning results container.
Definition: girebinning.c:4694
giraffe_rebinning_destroy
void giraffe_rebinning_destroy(GiRebinning *rebinning)
Destroys a rebinning results container and its contents.
Definition: girebinning.c:4788
giraffe_rebin_config_add
void giraffe_rebin_config_add(cpl_parameterlist *list)
Adds parameters for the rebinning.
Definition: girebinning.c:4950
giraffe_sgcalibration_config_create
GiSGCalConfig * giraffe_sgcalibration_config_create(cpl_parameterlist *list)
Creates a setup structure for the slit geometry calibration.
Definition: gisgcalibration.c:2428
giraffe_compute_offsets
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.
Definition: gisgcalibration.c:2185
giraffe_sgcalibration_config_destroy
void giraffe_sgcalibration_config_destroy(GiSGCalConfig *config)
Destroys a sgcalibration field setup structure.
Definition: gisgcalibration.c:2638
giraffe_sgcalibration_config_add
void giraffe_sgcalibration_config_add(cpl_parameterlist *list)
Adds parameters for the sgcalibration correction computation.
Definition: gisgcalibration.c:2669
giraffe_slitgeometry_load
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.
Definition: gislitgeometry.c:602
giraffe_table_new
GiTable * giraffe_table_new(void)
Creates a new, empty Giraffe table.
Definition: gitable.c:85
giraffe_table_duplicate
GiTable * giraffe_table_duplicate(const GiTable *src)
Duplicate a Giraffe table.
Definition: gitable.c:176
giraffe_table_load
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.
Definition: gitable.c:562
giraffe_table_delete
void giraffe_table_delete(GiTable *self)
Destroys a Giraffe table.
Definition: gitable.c:154
giraffe_table_get
cpl_table * giraffe_table_get(const GiTable *self)
Get the table data from a Giraffe table.
Definition: gitable.c:433
giraffe_add_frameset_info
cxint giraffe_add_frameset_info(cpl_propertylist *plist, const cpl_frameset *set, cxint sequence)
Add frameset specific information to a property list.
Definition: giutils.c:786
giraffe_propertylist_copy
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.
Definition: giutils.c:1108
giraffe_get_license
const cxchar * giraffe_get_license(void)
Get the pipeline copyright and license.
Definition: giutils.c:422
giraffe_get_mode
GiInstrumentMode giraffe_get_mode(cpl_propertylist *properties)
Determines the instrument mode from a property list.
Definition: giutils.c:444
GiSGCalConfig
Slit geometry calibration configuration data structure.
Definition: gisgcalibration.h:49
This file is part of the GIRAFFE Pipeline Reference Manual 2.19.4.
Documentation copyright © 2002-2006 European Southern Observatory.
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