GIRAFFE Pipeline Reference Manual

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_QCSCHEME, 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, GIALIAS_QCFLAG
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) {
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) {
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
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
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 status = 0;
810
811 localization->locy = giraffe_image_new(CPL_TYPE_DOUBLE);
812 status = giraffe_image_load(localization->locy, filename, 0);
813
814 if (status) {
815 cpl_msg_error(_id, "Cannot load localization (centroid "
816 "position) frame from '%s'. Aborting ...",
817 filename);
818
819 giraffe_localization_destroy(localization);
820
821 if (bpixel) {
822 giraffe_image_delete(bpixel);
823 bpixel = NULL;
824 }
825
826 giraffe_table_delete(fibers);
827 giraffe_image_delete(rscience);
828
829 return 1;
830 }
831
832
833 filename = cpl_frame_get_filename(locw_frame);
834 status = 0;
835
836 localization->locw = giraffe_image_new(CPL_TYPE_DOUBLE);
837 status = giraffe_image_load(localization->locw, filename, 0);
838
839 if (status) {
840 cpl_msg_error(_id, "Cannot load localization (spectrum width) "
841 "frame from '%s'. Aborting ...", filename);
842
843 giraffe_localization_destroy(localization);
844
845 if (bpixel) {
846 giraffe_image_delete(bpixel);
847 bpixel = NULL;
848 }
849
850 giraffe_table_delete(fibers);
851 giraffe_image_delete(rscience);
852
853 return 1;
854 }
855
856
857 /*
858 * Spectrum extraction
859 */
860
861 if (slight_frame) {
862
863 filename = cpl_frame_get_filename(slight_frame);
864
865
866 slight = giraffe_image_new(CPL_TYPE_DOUBLE);
867 status = giraffe_image_load(slight, filename, 0);
868
869 if (status) {
870 cpl_msg_error(_id, "Cannot load scattered light model from '%s'. "
871 "Aborting ...", filename);
872
873 giraffe_image_delete(slight);
874
875 giraffe_localization_destroy(localization);
876
877 if (bpixel) {
878 giraffe_image_delete(bpixel);
879 bpixel = NULL;
880 }
881
882 giraffe_table_delete(fibers);
883 giraffe_image_delete(rscience);
884
885 return 1;
886
887 }
888
889 }
890
891
892 extract_config = giraffe_extract_config_create(config);
893
894 if ((extract_config->emethod == GIEXTRACT_OPTIMAL) ||
895 (extract_config->emethod == GIEXTRACT_HORNE)) {
896
897 if (psfdata_frame == NULL) {
898
899 const cxchar* emethod = "Optimal";
900
901 if (extract_config->emethod == GIEXTRACT_HORNE) {
902 emethod = "Horne";
903 }
904
905 cpl_msg_error(_id, "%s spectrum extraction requires PSF "
906 "profile data. Aborting ...", emethod);
907
908 giraffe_extract_config_destroy(extract_config);
909 extract_config = NULL;
910
911 if (slight != NULL) {
912 giraffe_image_delete(slight);
913 slight = NULL;
914 }
915
916 giraffe_localization_destroy(localization);
917 localization = NULL;
918
919 if (bpixel) {
920 giraffe_image_delete(bpixel);
921 bpixel = NULL;
922 }
923
924 giraffe_table_delete(fibers);
925 fibers = NULL;
926
927 giraffe_image_delete(rscience);
928 rscience = NULL;
929
930 return 1;
931
932 }
933 else {
934
935 filename = cpl_frame_get_filename(psfdata_frame);
936 status = 0;
937
938 localization->psf = giraffe_psfdata_new();
939 status = giraffe_psfdata_load(localization->psf, filename);
940
941 if (status) {
942 cpl_msg_error(_id, "Cannot load PSF profile data frame from "
943 "'%s'. Aborting ...", filename);
944
945 giraffe_extract_config_destroy(extract_config);
946 extract_config = NULL;
947
948 if (slight != NULL) {
949 giraffe_image_delete(slight);
950 slight = NULL;
951 }
952
953 giraffe_localization_destroy(localization);
954 localization = NULL;
955
956 if (bpixel) {
957 giraffe_image_delete(bpixel);
958 bpixel = NULL;
959 }
960
961 giraffe_table_delete(fibers);
962 fibers = NULL;
963
964 giraffe_image_delete(rscience);
965 rscience = NULL;
966
967 return 1;
968
969 }
970
971 }
972
973 }
974
975
976 extraction = giraffe_extraction_new();
977
978 status = giraffe_extract_spectra(extraction, rscience, fibers,
979 localization, bpixel, slight,
980 extract_config);
981
982 if (status) {
983 cpl_msg_error(_id, "Spectrum extraction failed! Aborting ...");
984
985 giraffe_extraction_destroy(extraction);
986 giraffe_extract_config_destroy(extract_config);
987
988 giraffe_image_delete(slight);
989
990 giraffe_localization_destroy(localization);
991
992 if (bpixel) {
993 giraffe_image_delete(bpixel);
994 bpixel = NULL;
995 }
996
997 giraffe_table_delete(fibers);
998 giraffe_image_delete(rscience);
999
1000 return 1;
1001 }
1002
1003 giraffe_image_delete(slight);
1004 slight = NULL;
1005
1006 if (bpixel) {
1007 giraffe_image_delete(bpixel);
1008 bpixel = NULL;
1009 }
1010
1011 giraffe_image_delete(rscience);
1012 rscience = NULL;
1013
1014 giraffe_extract_config_destroy(extract_config);
1015
1016
1017 /*
1018 * Apply flat field and apply the relative fiber transmission correction.
1019 */
1020
1021 flat_config = giraffe_flat_config_create(config);
1022
1023 if (flat_config->load == TRUE) {
1024
1025 cpl_frame* flat_frame = NULL;
1026
1027 GiImage* flat = NULL;
1028
1029
1030 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTSPECTRA);
1031
1032 if (flat_frame == NULL) {
1033 cpl_msg_error(_id, "Missing flat field spectra frame!");
1034
1035 giraffe_flat_config_destroy(flat_config);
1036
1037 giraffe_extraction_destroy(extraction);
1038 giraffe_localization_destroy(localization);
1039
1040 giraffe_table_delete(wcalcoeff);
1041
1042 giraffe_table_delete(grating);
1043 giraffe_table_delete(fibers);
1044
1045 return 1;
1046 }
1047
1048 filename = cpl_frame_get_filename(flat_frame);
1049
1050 flat = giraffe_image_new(CPL_TYPE_DOUBLE);
1051 status = giraffe_image_load(flat, filename, 0);
1052
1053 if (status) {
1054 cpl_msg_error(_id, "Cannot load flat field spectra from '%s'. "
1055 "Aborting ...", filename);
1056
1058
1059 giraffe_flat_config_destroy(flat_config);
1060
1061 giraffe_extraction_destroy(extraction);
1062 giraffe_localization_destroy(localization);
1063
1064 giraffe_table_delete(wcalcoeff);
1065
1066 giraffe_table_delete(grating);
1067 giraffe_table_delete(fibers);
1068
1069 return 1;
1070 }
1071
1072 if (flat_config->apply == TRUE) {
1073
1074 GiImage* errors = NULL;
1075
1076
1077 flat_frame = cpl_frameset_find(set, GIFRAME_FIBER_FLAT_EXTERRORS);
1078
1079 if (flat_frame == NULL) {
1080 cpl_msg_warning(_id, "Missing flat field spectra errors "
1081 "frame!");
1082 }
1083 else {
1084
1085 filename = cpl_frame_get_filename(flat_frame);
1086
1087 errors = giraffe_image_new(CPL_TYPE_DOUBLE);
1088 status = giraffe_image_load(errors, filename, 0);
1089
1090 if (status) {
1091 cpl_msg_error(_id, "Cannot load flat field spectra "
1092 "errors from '%s'. Aborting ...",
1093 filename);
1094
1095 giraffe_image_delete(errors);
1097
1098 giraffe_flat_config_destroy(flat_config);
1099
1100 giraffe_extraction_destroy(extraction);
1101 giraffe_localization_destroy(localization);
1102
1103 giraffe_table_delete(wcalcoeff);
1104
1105 giraffe_table_delete(grating);
1106 giraffe_table_delete(fibers);
1107
1108 return 1;
1109 }
1110
1111 }
1112
1113 cpl_msg_info(_id, "Applying flat field correction ...");
1114
1115 status = giraffe_flat_apply(extraction, fibers, flat, errors,
1116 flat_config);
1117
1118 if (status) {
1119 cpl_msg_error(_id, "Flat field correction failed! "
1120 "Aborting ...");
1121
1122 giraffe_image_delete(errors);
1124
1125 giraffe_flat_config_destroy(flat_config);
1126
1127 giraffe_extraction_destroy(extraction);
1128 giraffe_localization_destroy(localization);
1129
1130 giraffe_table_delete(wcalcoeff);
1131
1132 giraffe_table_delete(grating);
1133 giraffe_table_delete(fibers);
1134
1135 return 1;
1136 }
1137
1138 giraffe_image_delete(errors);
1139 errors = NULL;
1140
1141 }
1142
1143 if (flat_config->transmission == TRUE) {
1144
1145 const cxchar* _filename = cpl_frame_get_filename(flat_frame);
1146
1147 GiTable* _fibers = NULL;
1148
1149
1150 cpl_msg_info(_id, "Loading fiber setup for frame '%s'.",
1151 _filename);
1152
1153 _fibers = giraffe_fiberlist_load(_filename, 1, "FIBER_SETUP");
1154
1155 if (!_fibers) {
1156 cpl_msg_error(_id, "Cannot create fiber setup for "
1157 "frame '%s'! Aborting ...", _filename);
1158
1160
1161 giraffe_flat_config_destroy(flat_config);
1162
1163 giraffe_extraction_destroy(extraction);
1164 giraffe_localization_destroy(localization);
1165
1166 giraffe_table_delete(wcalcoeff);
1167
1168 giraffe_table_delete(grating);
1169 giraffe_table_delete(fibers);
1170
1171 return 1;
1172 }
1173
1174 cpl_msg_info(_id, "Applying relative fiber transmission "
1175 "correction");
1176
1177 status = giraffe_transmission_setup(fibers, _fibers);
1178 giraffe_table_delete(_fibers);
1179
1180 if (status == 0) {
1181 status = giraffe_transmission_apply(extraction, fibers);
1182 }
1183
1184 if (status) {
1185
1186 cpl_msg_error(_id, "Relative transmission correction failed! "
1187 "Aborting ...");
1188
1190
1191 giraffe_flat_config_destroy(flat_config);
1192
1193 giraffe_extraction_destroy(extraction);
1194 giraffe_localization_destroy(localization);
1195
1196 giraffe_table_delete(wcalcoeff);
1197
1198 giraffe_table_delete(grating);
1199 giraffe_table_delete(fibers);
1200
1201 return 1;
1202
1203 }
1204
1205 }
1206
1208
1209 }
1210
1211 giraffe_flat_config_destroy(flat_config);
1212
1213
1214 /*
1215 * Save the spectrum extraction results and register them as
1216 * products.
1217 */
1218
1219 cpl_msg_info(_id, "Writing extracted spectra ...");
1220
1221 /* Extracted spectra */
1222
1223 giraffe_image_add_info(extraction->spectra, &info, set);
1224
1225 cpl_propertylist* extprop = giraffe_image_get_properties(extraction->spectra);
1226
1227 giraffe_qc_update_sci_props(extprop, fibers);
1228
1229
1230 sext_frame = giraffe_frame_create_image(extraction->spectra,
1231 GIFRAME_SCIENCE_EXTSPECTRA,
1232 CPL_FRAME_LEVEL_FINAL,
1233 TRUE, TRUE);
1234
1235 if (sext_frame == NULL) {
1236 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1237
1238 giraffe_extraction_destroy(extraction);
1239 giraffe_localization_destroy(localization);
1240
1241 giraffe_table_delete(wcalcoeff);
1242
1243 giraffe_table_delete(grating);
1244 giraffe_table_delete(fibers);
1245
1246 return 1;
1247 }
1248
1249 status = giraffe_fiberlist_attach(sext_frame, fibers);
1250
1251 if (status) {
1252 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1253 "Aborting ...", cpl_frame_get_filename(sext_frame));
1254
1255 cpl_frame_delete(sext_frame);
1256
1257 giraffe_extraction_destroy(extraction);
1258 giraffe_localization_destroy(localization);
1259
1260 giraffe_table_delete(wcalcoeff);
1261
1262 giraffe_table_delete(grating);
1263 giraffe_table_delete(fibers);
1264
1265 return 1;
1266 }
1267
1268 cpl_frameset_insert(set, sext_frame);
1269
1270 /* Extracted spectra errors */
1271
1272
1273
1274 cpl_propertylist* exterrprop = giraffe_image_get_properties(extraction->error);
1275
1276 giraffe_qc_update_sci_props(exterrprop, fibers);
1277
1278
1279 giraffe_image_add_info(extraction->error, &info, set);
1280
1281 sext_frame = giraffe_frame_create_image(extraction->error,
1282 GIFRAME_SCIENCE_EXTERRORS,
1283 CPL_FRAME_LEVEL_FINAL,
1284 TRUE, TRUE);
1285
1286 if (sext_frame == NULL) {
1287 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1288
1289 giraffe_extraction_destroy(extraction);
1290 giraffe_localization_destroy(localization);
1291
1292 giraffe_table_delete(wcalcoeff);
1293
1294 giraffe_table_delete(grating);
1295 giraffe_table_delete(fibers);
1296
1297 return 1;
1298 }
1299
1300 status = giraffe_fiberlist_attach(sext_frame, fibers);
1301
1302 if (status) {
1303 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1304 "Aborting ...", cpl_frame_get_filename(sext_frame));
1305
1306 cpl_frame_delete(sext_frame);
1307
1308 giraffe_extraction_destroy(extraction);
1309 giraffe_localization_destroy(localization);
1310
1311 giraffe_table_delete(wcalcoeff);
1312
1313 giraffe_table_delete(grating);
1314 giraffe_table_delete(fibers);
1315
1316 return 1;
1317 }
1318
1319 cpl_frameset_insert(set, sext_frame);
1320
1321 /* Extracted spectra pixels */
1322
1323 if (extraction->npixels != NULL) {
1324
1325 cpl_propertylist* extpixprop = giraffe_image_get_properties(extraction->npixels);
1326
1327 giraffe_qc_update_sci_props(extpixprop, fibers);
1328
1329 giraffe_image_add_info(extraction->npixels, &info, set);
1330
1331 sext_frame = giraffe_frame_create_image(extraction->npixels,
1332 GIFRAME_SCIENCE_EXTPIXELS,
1333 CPL_FRAME_LEVEL_FINAL,
1334 TRUE, TRUE);
1335
1336 if (sext_frame == NULL) {
1337 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1338
1339 giraffe_extraction_destroy(extraction);
1340 giraffe_localization_destroy(localization);
1341
1342 giraffe_table_delete(wcalcoeff);
1343
1344 giraffe_table_delete(grating);
1345 giraffe_table_delete(fibers);
1346
1347 return 1;
1348 }
1349
1350 status = giraffe_fiberlist_attach(sext_frame, fibers);
1351
1352 if (status) {
1353 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1354 "Aborting ...", cpl_frame_get_filename(sext_frame));
1355
1356 cpl_frame_delete(sext_frame);
1357
1358 giraffe_extraction_destroy(extraction);
1359 giraffe_localization_destroy(localization);
1360
1361 giraffe_table_delete(wcalcoeff);
1362
1363 giraffe_table_delete(grating);
1364 giraffe_table_delete(fibers);
1365
1366 return 1;
1367 }
1368
1369 cpl_frameset_insert(set, sext_frame);
1370
1371 }
1372
1373 /* Extracted spectra centroids */
1374
1375 giraffe_image_add_info(extraction->centroid, &info, set);
1376
1377 sext_frame = giraffe_frame_create_image(extraction->centroid,
1378 GIFRAME_SCIENCE_EXTTRACE,
1379 CPL_FRAME_LEVEL_FINAL,
1380 TRUE, TRUE);
1381
1382 if (sext_frame == NULL) {
1383 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1384
1385 giraffe_extraction_destroy(extraction);
1386 giraffe_localization_destroy(localization);
1387
1388 giraffe_table_delete(wcalcoeff);
1389
1390 giraffe_table_delete(grating);
1391 giraffe_table_delete(fibers);
1392
1393 return 1;
1394 }
1395
1396 status = giraffe_fiberlist_attach(sext_frame, fibers);
1397
1398 if (status) {
1399 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1400 "Aborting ...", cpl_frame_get_filename(sext_frame));
1401
1402 cpl_frame_delete(sext_frame);
1403
1404 giraffe_extraction_destroy(extraction);
1405 giraffe_localization_destroy(localization);
1406
1407 giraffe_table_delete(wcalcoeff);
1408
1409 giraffe_table_delete(grating);
1410 giraffe_table_delete(fibers);
1411
1412 return 1;
1413 }
1414
1415 cpl_frameset_insert(set, sext_frame);
1416
1417 /* Extraction model spectra */
1418
1419 if (extraction->model != NULL) {
1420
1421 giraffe_image_add_info(extraction->model, &info, set);
1422
1423 sext_frame = giraffe_frame_create_image(extraction->model,
1424 GIFRAME_SCIENCE_EXTMODEL,
1425 CPL_FRAME_LEVEL_FINAL,
1426 TRUE, TRUE);
1427
1428 if (sext_frame == NULL) {
1429 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1430
1431 giraffe_extraction_destroy(extraction);
1432 giraffe_localization_destroy(localization);
1433
1434 giraffe_table_delete(wcalcoeff);
1435
1436 giraffe_table_delete(grating);
1437 giraffe_table_delete(fibers);
1438
1439 return 1;
1440 }
1441
1442 status = giraffe_fiberlist_attach(sext_frame, fibers);
1443
1444 if (status != 0) {
1445 cpl_msg_error(_id, "Cannot attach fiber setup to local file '%s'! "
1446 "Aborting ...", cpl_frame_get_filename(sext_frame));
1447
1448 cpl_frame_delete(sext_frame);
1449
1450 giraffe_extraction_destroy(extraction);
1451 giraffe_localization_destroy(localization);
1452
1453 giraffe_table_delete(wcalcoeff);
1454
1455 giraffe_table_delete(grating);
1456 giraffe_table_delete(fibers);
1457
1458 return 1;
1459 }
1460
1461 cpl_frameset_insert(set, sext_frame);
1462
1463 }
1464
1465
1466 /*
1467 * Load dispersion solution
1468 */
1469
1470
1471 filename = (cxchar *)cpl_frame_get_filename(wcal_frame);
1472
1473 tempes = cpl_errorstate_get();
1474
1475 const char qcdltcopy[] = "^(ESO INS TEMP53 VAL|MJD-OBS)$";
1476 cpl_propertylist * qcdltlist = cpl_propertylist_load_regexp(filename, 0,
1477 qcdltcopy, 0);
1478 cpl_errorstate_set(tempes);
1479
1480 wcalcoeff = giraffe_table_new();
1481 status = giraffe_table_load(wcalcoeff, filename, 1, NULL);
1482
1483 if (status) {
1484 cpl_msg_error(_id, "Cannot load dispersion solution from "
1485 "'%s'. Aborting ...", filename);
1486
1487 giraffe_extraction_destroy(extraction);
1488 giraffe_localization_destroy(localization);
1489
1490 giraffe_table_delete(wcalcoeff);
1491
1492 giraffe_table_delete(grating);
1493 giraffe_table_delete(fibers);
1494
1495 return 1;
1496 }
1497
1498
1499 /*
1500 * Load grating data
1501 */
1502
1503 filename = (cxchar *)cpl_frame_get_filename(grating_frame);
1504
1505 status = 0;
1506
1507 grating = giraffe_table_new();
1508 status = giraffe_table_load(grating, filename, 1, NULL);
1509
1510 if (status) {
1511 cpl_msg_error(_id, "Cannot load grating data from '%s'. "
1512 "Aborting ...", filename);
1513
1514 giraffe_extraction_destroy(extraction);
1515 giraffe_localization_destroy(localization);
1516
1517 giraffe_table_delete(wcalcoeff);
1518
1519 giraffe_table_delete(grating);
1520 giraffe_table_delete(fibers);
1521
1522 return 1;
1523 }
1524
1525
1526 /*
1527 * Load slit geometry data
1528 */
1529
1530
1531 filename = (cxchar *)cpl_frame_get_filename(slit_frame);
1532
1533 slitgeometry = giraffe_slitgeometry_load(fibers, filename, 1, NULL);
1534
1535 if (slitgeometry == NULL) {
1536 cpl_msg_error(_id, "Cannot load slit geometry data from '%s'. "
1537 "Aborting ...", filename);
1538
1539 giraffe_table_delete(wcalcoeff);
1540
1541 giraffe_extraction_destroy(extraction);
1542 giraffe_localization_destroy(localization);
1543
1544 giraffe_table_delete(wcalcoeff);
1545
1546 giraffe_table_delete(grating);
1547 giraffe_table_delete(fibers);
1548
1549 return 1;
1550 }
1551 else {
1552
1553 /*
1554 * Check whether the contains the positions for all fibers
1555 * provided by the fiber setup. If this is not the case
1556 * this is an error.
1557 */
1558
1559 if (giraffe_fiberlist_compare(slitgeometry, fibers) != 1) {
1560 cpl_msg_error(_id, "Slit geometry data from '%s' is not "
1561 "applicable for current fiber setup! "
1562 "Aborting ...", filename);
1563
1564 giraffe_table_delete(slitgeometry);
1565 giraffe_table_delete(wcalcoeff);
1566
1567 giraffe_extraction_destroy(extraction);
1568 giraffe_localization_destroy(localization);
1569
1570 giraffe_table_delete(wcalcoeff);
1571
1572 giraffe_table_delete(grating);
1573 giraffe_table_delete(fibers);
1574
1575 return 1;
1576 }
1577
1578 }
1579
1580
1581
1582 /*
1583 * Spectrum rebinning
1584 */
1585
1586 cpl_msg_info(_id, "Spectrum rebinning");
1587
1588 rebin_config = giraffe_rebin_config_create(config);
1589
1590 rebinning = giraffe_rebinning_new();
1591
1592 status = giraffe_rebin_spectra(rebinning, extraction, fibers,
1593 localization, grating, slitgeometry,
1594 wcalcoeff, rebin_config);
1595
1596 if (status) {
1597 cpl_msg_error(_id, "Rebinning of science spectra failed! Aborting...");
1598
1599 giraffe_rebinning_destroy(rebinning);
1600
1601 giraffe_extraction_destroy(extraction);
1602 giraffe_localization_destroy(localization);
1603
1604 giraffe_table_delete(wcalcoeff);
1605
1606 giraffe_table_delete(slitgeometry);
1607 giraffe_table_delete(grating);
1608 giraffe_table_delete(fibers);
1609
1610 giraffe_rebin_config_destroy(rebin_config);
1611
1612 return 1;
1613
1614 }
1615
1616
1617 /*
1618 * Optionally compute and apply spectral shifts from the simultaneous
1619 * calibration fibers. This is only done if the simultaneous calibration
1620 * fibers were used.
1621 */
1622
1623 p = cpl_parameterlist_find(config, "giraffe.siwc.apply");
1624 cx_assert(p != NULL);
1625
1626 siwc = cpl_parameter_get_bool(p);
1627 p = NULL;
1628
1629 properties = giraffe_image_get_properties(rebinning->spectra);
1630 cx_assert(properties != NULL);
1631
1632
1633 if (cpl_propertylist_has(properties, GIALIAS_STSCTAL) == TRUE) {
1634 calsim = cpl_propertylist_get_bool(properties, GIALIAS_STSCTAL);
1635 }
1636
1637
1638 if ((siwc == TRUE) && (calsim == TRUE) && (linemask_frame != NULL)) {
1639
1640 GiTable* linemask = giraffe_table_new();
1641
1642 GiSGCalConfig* siwc_config = NULL;
1643
1644
1645 siwc_config = giraffe_sgcalibration_config_create(config);
1646
1647 if (siwc_config == NULL) {
1648
1649 giraffe_table_delete(linemask);
1650 linemask = NULL;
1651
1652 giraffe_rebinning_destroy(rebinning);
1653
1654 giraffe_extraction_destroy(extraction);
1655 giraffe_localization_destroy(localization);
1656
1657 giraffe_table_delete(wcalcoeff);
1658
1659 giraffe_table_delete(slitgeometry);
1660 giraffe_table_delete(grating);
1661 giraffe_table_delete(fibers);
1662
1663 giraffe_rebin_config_destroy(rebin_config);
1664
1665 return 1;
1666
1667 }
1668
1669 filename = cpl_frame_get_filename(linemask_frame);
1670
1671 status = giraffe_table_load(linemask, filename, 1, NULL);
1672
1673 if (status) {
1674 cpl_msg_error(_id, "Cannot load line reference mask from '%s'. "
1675 "Aborting ...", filename);
1676
1678 siwc_config = NULL;
1679
1680 giraffe_table_delete(linemask);
1681 linemask = NULL;
1682
1683 giraffe_rebinning_destroy(rebinning);
1684
1685 giraffe_extraction_destroy(extraction);
1686 giraffe_localization_destroy(localization);
1687
1688 giraffe_table_delete(wcalcoeff);
1689
1690 giraffe_table_delete(slitgeometry);
1691 giraffe_table_delete(grating);
1692 giraffe_table_delete(fibers);
1693
1694 giraffe_rebin_config_destroy(rebin_config);
1695
1696 return 1;
1697
1698 }
1699
1700
1701 status = giraffe_compute_offsets(fibers, rebinning, grating,
1702 linemask, siwc_config);
1703
1704 if (status != 0) {
1705 cpl_msg_error(_id, "Applying simultaneous wavelength "
1706 "calibration correction failed! Aborting...");
1707
1709 siwc_config = NULL;
1710
1711 giraffe_table_delete(linemask);
1712 linemask = NULL;
1713
1714 giraffe_rebinning_destroy(rebinning);
1715
1716 giraffe_extraction_destroy(extraction);
1717 giraffe_localization_destroy(localization);
1718
1719 giraffe_table_delete(wcalcoeff);
1720
1721 giraffe_table_delete(slitgeometry);
1722 giraffe_table_delete(grating);
1723 giraffe_table_delete(fibers);
1724
1725 giraffe_rebin_config_destroy(rebin_config);
1726
1727 return 1;
1728
1729 }
1730
1732 siwc_config = NULL;
1733
1734 giraffe_table_delete(linemask);
1735 linemask = NULL;
1736
1737 giraffe_rebinning_destroy(rebinning);
1738 rebinning = giraffe_rebinning_new();
1739
1740 status = giraffe_rebin_spectra(rebinning, extraction, fibers,
1741 localization, grating, slitgeometry,
1742 wcalcoeff, rebin_config);
1743
1744 if (status) {
1745 cpl_msg_error(_id, "Rebinning of science spectra failed! "
1746 "Aborting...");
1747
1748 giraffe_rebinning_destroy(rebinning);
1749
1750 giraffe_extraction_destroy(extraction);
1751 giraffe_localization_destroy(localization);
1752
1753 giraffe_table_delete(wcalcoeff);
1754
1755 giraffe_table_delete(slitgeometry);
1756 giraffe_table_delete(grating);
1757 giraffe_table_delete(fibers);
1758
1759 giraffe_rebin_config_destroy(rebin_config);
1760
1761 return 1;
1762
1763 }
1764
1765 }
1766
1767 giraffe_extraction_destroy(extraction);
1768 extraction = NULL;
1769
1770 giraffe_localization_destroy(localization);
1771 localization = NULL;
1772
1773 giraffe_rebin_config_destroy(rebin_config);
1774 rebin_config = NULL;
1775
1776
1777 /*
1778 * Compute barycentric correction for each object spectrum (fiber)
1779 */
1780
1781 status = giraffe_add_rvcorrection(fibers, rebinning->spectra);
1782
1783 switch (status) {
1784 case 0:
1785 {
1786 break;
1787 }
1788
1789 case 1:
1790 {
1791 cpl_msg_warning(_id, "Missing observation time properties! "
1792 "Barycentric correction computation "
1793 "skipped!");
1794 status = 0;
1795 break;
1796 }
1797 case 2:
1798 {
1799 cpl_msg_warning(_id, "Missing telescope location properties! "
1800 "Barycentric correction computation "
1801 "skipped!");
1802 status = 0;
1803 break;
1804 }
1805 case 3:
1806 {
1807 cpl_msg_warning(_id, "Object positions are not available "
1808 "Barycentric correction computation "
1809 "skipped!");
1810 status = 0;
1811 break;
1812 }
1813 default:
1814 {
1815 cpl_msg_error(_id, "Barycentric correction computation "
1816 "failed! Aborting...");
1817
1818 giraffe_rebinning_destroy(rebinning);
1819
1820 giraffe_table_delete(wcalcoeff);
1821
1822 giraffe_table_delete(slitgeometry);
1823 giraffe_table_delete(grating);
1824 giraffe_table_delete(fibers);
1825
1826 return 1;
1827 break;
1828 }
1829
1830 }
1831
1832
1833 /*
1834 * Save and register the results of the spectrum rebinning.
1835 */
1836
1837 /* Rebinned spectra */
1838
1839 /*
1840 * Add the QC parameters to the rebinning spectra
1841 */
1842
1843 tempes = cpl_errorstate_get();
1844
1845 cpl_propertylist* rbprop = giraffe_image_get_properties(rebinning->spectra);
1846
1847
1848 giraffe_propertylist_copy(rbprop, GIALIAS_WLSTART, rbprop,
1849 GIALIAS_BINWLMIN);
1850 giraffe_propertylist_copy(rbprop, GIALIAS_WLEND, rbprop,
1851 GIALIAS_BINWLMAX);
1852 giraffe_propertylist_copy(rbprop, GIALIAS_WLSTEP, rbprop,
1853 GIALIAS_BINSTEP);
1854
1855 double dlttemp = cpl_propertylist_get_double(rbprop, "ESO INS TEMP53 VAL");
1856 dlttemp -= cpl_propertylist_get_double(qcdltlist, "ESO INS TEMP53 VAL");
1857
1858 double dltdate = cpl_propertylist_get_double(rbprop, "MJD-OBS");
1859 dltdate -= cpl_propertylist_get_double(qcdltlist, "MJD-OBS");
1860
1861 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTEMP, dlttemp);
1862 cpl_propertylist_append_double(rbprop, GIALIAS_QCDLTTIME, dltdate);
1863
1864 /*
1865 * For the QC_FLAG bitmask a value of 1 represents an issue
1866 * so we initialise the bitmask to all bits set to 1
1867 */
1868
1869 int nbits = 5;
1870
1871 int bitmask = pow(2, nbits) - 1;
1872
1873 if (-1.5 < dlttemp && dlttemp < 1.5) {
1874 bitmask &= ~0x1;
1875 }
1876
1877 if (-1.0 < dltdate && dltdate < 1.0) {
1878 bitmask &= ~0x2;
1879 }
1880
1881 if (nsaturated < 1000){
1882 bitmask &= ~0x4;
1883 }
1884
1885 if (cpl_propertylist_get_int(rbprop, GIALIAS_QCNFIBSCI) >= 10) {
1886 bitmask &= ~0x8;
1887 }
1888
1889 if (cpl_propertylist_get_int(rbprop, GIALIAS_QCNFIBSKY) >= 1) {
1890 bitmask &= ~0x10;
1891 }
1892
1893 /*
1894 * The bitmask is stored as a string in the fits header, with the
1895 * least significant bit first.
1896 */
1897
1898 char bitmaskstr[nbits + 1];
1899
1900 for (int biti = 0; biti < nbits; biti++) {
1901 bitmaskstr[biti] = (bitmask & (1 << biti)) ? '1' : '0';
1902 }
1903 bitmaskstr[nbits] = '\0';
1904
1905 cpl_propertylist_append_string(rbprop, GIALIAS_QCFLAG, bitmaskstr);
1906
1907 cpl_errorstate_set(tempes);
1908
1909 giraffe_image_add_info(rebinning->spectra, &info, set);
1910
1911 rbin_frame = giraffe_frame_create_image(rebinning->spectra,
1912 GIFRAME_SCIENCE_RBNSPECTRA,
1913 CPL_FRAME_LEVEL_FINAL,
1914 TRUE, TRUE);
1915
1916 if (rbin_frame == NULL) {
1917 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1918
1919 giraffe_rebinning_destroy(rebinning);
1920
1921 giraffe_table_delete(wcalcoeff);
1922
1923 giraffe_table_delete(slitgeometry);
1924 giraffe_table_delete(grating);
1925 giraffe_table_delete(fibers);
1926
1927 return 1;
1928 }
1929
1930 status = giraffe_fiberlist_attach(rbin_frame, fibers);
1931
1932 if (status) {
1933 cpl_msg_error(_id, "Cannot attach fiber setup to local "
1934 "file '%s'! Aborting ...",
1935 cpl_frame_get_filename(rbin_frame));
1936
1937 giraffe_rebinning_destroy(rebinning);
1938 giraffe_table_delete(wcalcoeff);
1939
1940 giraffe_table_delete(slitgeometry);
1941 giraffe_table_delete(grating);
1942 giraffe_table_delete(fibers);
1943
1944 cpl_frame_delete(rbin_frame);
1945
1946 return 1;
1947 }
1948
1949 cpl_frameset_insert(set, rbin_frame);
1950 flux_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
1951
1952 /* Rebinned spectra errors */
1953
1954 tempes = cpl_errorstate_get();
1955
1956 cpl_propertylist* rberrprop = giraffe_image_get_properties(rebinning->errors);
1957
1958
1959 giraffe_propertylist_copy(rberrprop, GIALIAS_WLSTART, rberrprop,
1960 GIALIAS_BINWLMIN);
1961 giraffe_propertylist_copy(rberrprop, GIALIAS_WLEND, rberrprop,
1962 GIALIAS_BINWLMAX);
1963 giraffe_propertylist_copy(rberrprop, GIALIAS_WLSTEP, rberrprop,
1964 GIALIAS_BINSTEP);
1965
1966 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTEMP, dlttemp);
1967 cpl_propertylist_append_double(rberrprop, GIALIAS_QCDLTTIME, dltdate);
1968
1969 cpl_propertylist_append_string(rberrprop, GIALIAS_QCFLAG, bitmaskstr);
1970
1971 giraffe_image_add_info(rebinning->errors, &info, set);
1972
1973 cpl_errorstate_set(tempes);
1974
1975 rbin_frame = giraffe_frame_create_image(rebinning->errors,
1976 GIFRAME_SCIENCE_RBNERRORS,
1977 CPL_FRAME_LEVEL_FINAL,
1978 TRUE, TRUE);
1979
1980 if (rbin_frame == NULL) {
1981 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
1982
1983 giraffe_rebinning_destroy(rebinning);
1984
1985 giraffe_table_delete(wcalcoeff);
1986
1987 giraffe_table_delete(slitgeometry);
1988 giraffe_table_delete(grating);
1989 giraffe_table_delete(fibers);
1990 cpl_free(flux_filename);
1991
1992 return 1;
1993 }
1994
1995 status = giraffe_fiberlist_attach(rbin_frame, fibers);
1996
1997 if (status) {
1998 cpl_msg_error(_id, "Cannot attach fiber setup to local "
1999 "file '%s'! Aborting ...",
2000 cpl_frame_get_filename(rbin_frame));
2001
2002 giraffe_rebinning_destroy(rebinning);
2003
2004 giraffe_table_delete(wcalcoeff);
2005
2006 giraffe_table_delete(slitgeometry);
2007 giraffe_table_delete(grating);
2008 giraffe_table_delete(fibers);
2009
2010 cpl_frame_delete(rbin_frame);
2011 cpl_free(flux_filename);
2012
2013 return 1;
2014 }
2015
2016 cpl_frameset_insert(set, rbin_frame);
2017 err_filename = cpl_strdup(cpl_frame_get_filename(rbin_frame));
2018
2019 properties = giraffe_image_get_properties(rebinning->spectra);
2020 mode = giraffe_get_mode(properties);
2021
2022 /*
2023 * Optionally generate spectra in Science Data Product (SDP) format.
2024 */
2025 p = cpl_parameterlist_find(config, "giraffe.sdp.format.generate");
2026 cx_assert(p != NULL);
2027 gensdp = cpl_parameter_get_bool(p);
2028 p = cpl_parameterlist_find(config, "giraffe.sdp.nassoc.keys");
2029 cx_assert(p != NULL);
2030 nassoc_keys = cpl_parameter_get_int(p);
2031 p = NULL;
2032 if (gensdp) {
2033 if (mode == GIMODE_MEDUSA) {
2034 status = _giraffe_make_sdp_spectra(flux_filename, err_filename,
2035 nassoc_keys, set, config, _id);
2036 if (status) {
2037 cpl_msg_error(_id, "Failed to generate spectra in Science Data"
2038 " Product format.");
2039
2040 giraffe_rebinning_destroy(rebinning);
2041
2042 giraffe_table_delete(wcalcoeff);
2043
2044 giraffe_table_delete(slitgeometry);
2045 giraffe_table_delete(grating);
2046 giraffe_table_delete(fibers);
2047
2048 cpl_free(flux_filename);
2049 cpl_free(err_filename);
2050
2051 return 1;
2052 }
2053 } else {
2054 cpl_msg_warning(_id, "Requested to generate SDP 1D spectra, but"
2055 " this is currently only supported for the MEDUSA"
2056 " mode. Skipping SDP generation.");
2057 }
2058 }
2059 cpl_free(flux_filename);
2060 cpl_free(err_filename);
2061
2062
2063 /*
2064 * Optional image and data cube construction (only for IFU and Argus)
2065 */
2066
2067 if (mode == GIMODE_IFU || mode == GIMODE_ARGUS) {
2068
2069 cpl_frame* rimg_frame = NULL;
2070
2071 GiFieldOfView* fov = NULL;
2072
2073 GiFieldOfViewConfig* fov_config = NULL;
2074
2075 GiFieldOfViewCubeFormat cube_format = GIFOV_FORMAT_ESO3D;
2076
2077
2078 fov_config = giraffe_fov_config_create(config);
2079
2080 cube_format = fov_config->format;
2081
2082
2083 cpl_msg_info(_id, "Reconstructing image and data cube from rebinned "
2084 "spectra ...");
2085
2086 fov = giraffe_fov_new();
2087
2088 status = giraffe_fov_build(fov, rebinning, fibers, wcalcoeff, grating,
2089 slitgeometry, fov_config);
2090
2091 if (status) {
2092
2093 if (status == -2) {
2094 cpl_msg_warning(_id, "No reconstructed image was built. "
2095 "Fiber list has no fiber position "
2096 "information.");
2097 }
2098 else {
2099 cpl_msg_error(_id, "Image reconstruction failed! Aborting...");
2100
2101 giraffe_fov_delete(fov);
2102 giraffe_rebinning_destroy(rebinning);
2103
2104 giraffe_table_delete(wcalcoeff);
2105
2106 giraffe_table_delete(slitgeometry);
2107 giraffe_table_delete(grating);
2108 giraffe_table_delete(fibers);
2109
2110 giraffe_fov_config_destroy(fov_config);
2111
2112 return 1;
2113 }
2114
2115 }
2116
2117 giraffe_fov_config_destroy(fov_config);
2118
2119
2120 /*
2121 * Save and register the results of the image reconstruction.
2122 */
2123
2124 /* Reconstructed image */
2125
2126 giraffe_image_add_info(fov->fov.spectra, &info, set);
2127
2128 rimg_frame = giraffe_frame_create_image(fov->fov.spectra,
2129 GIFRAME_SCIENCE_RCSPECTRA,
2130 CPL_FRAME_LEVEL_FINAL,
2131 TRUE, TRUE);
2132
2133 if (rimg_frame == NULL) {
2134 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2135
2136 giraffe_fov_delete(fov);
2137 giraffe_rebinning_destroy(rebinning);
2138
2139 giraffe_table_delete(wcalcoeff);
2140
2141 giraffe_table_delete(slitgeometry);
2142 giraffe_table_delete(grating);
2143 giraffe_table_delete(fibers);
2144
2145 return 1;
2146 }
2147
2148 cpl_frameset_insert(set, rimg_frame);
2149
2150
2151 /* Reconstructed image errors */
2152
2153 giraffe_image_add_info(fov->fov.errors, &info, set);
2154
2155 rimg_frame = giraffe_frame_create_image(fov->fov.errors,
2156 GIFRAME_SCIENCE_RCERRORS,
2157 CPL_FRAME_LEVEL_FINAL,
2158 TRUE, TRUE);
2159
2160 if (rimg_frame == NULL) {
2161 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2162
2163 giraffe_fov_delete(fov);
2164 giraffe_rebinning_destroy(rebinning);
2165
2166 giraffe_table_delete(wcalcoeff);
2167
2168 giraffe_table_delete(slitgeometry);
2169 giraffe_table_delete(grating);
2170 giraffe_table_delete(fibers);
2171
2172 return 1;
2173 }
2174
2175 cpl_frameset_insert(set, rimg_frame);
2176
2177
2178 /* Save data cubes according to format selection */
2179
2180 if (cube_format == GIFOV_FORMAT_SINGLE) {
2181
2182 /* Spectrum cube */
2183
2184 if (fov->cubes.spectra != NULL) {
2185
2186 cxint component = 0;
2187
2188 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes;
2189
2190
2191 properties = giraffe_image_get_properties(rebinning->spectra);
2192 properties = cpl_propertylist_duplicate(properties);
2193
2194 giraffe_add_frameset_info(properties, set, info.sequence);
2195
2196 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE_SPECTRA,
2197 CPL_FRAME_LEVEL_FINAL,
2198 properties,
2199 fov,
2200 &component,
2201 creator);
2202
2203 cpl_propertylist_delete(properties);
2204 properties = NULL;
2205
2206 if (rimg_frame == NULL) {
2207 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2208
2209 giraffe_fov_delete(fov);
2210 fov = NULL;
2211
2212 giraffe_rebinning_destroy(rebinning);
2213 rebinning = NULL;
2214
2215 giraffe_table_delete(wcalcoeff);
2216 wcalcoeff = NULL;
2217
2218 giraffe_table_delete(slitgeometry);
2219 slitgeometry = NULL;
2220
2221 giraffe_table_delete(grating);
2222 grating = NULL;
2223
2224 giraffe_table_delete(fibers);
2225 fibers = NULL;
2226
2227 return 1;
2228 }
2229
2230 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2231
2232 if (status != 0) {
2233 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2234 "file '%s'! Aborting ...",
2235 cpl_frame_get_filename(rimg_frame));
2236
2237 cpl_frame_delete(rimg_frame);
2238
2239 giraffe_fov_delete(fov);
2240 fov = NULL;
2241
2242 giraffe_rebinning_destroy(rebinning);
2243 rebinning = NULL;
2244
2245 giraffe_table_delete(wcalcoeff);
2246 wcalcoeff = NULL;
2247
2248 giraffe_table_delete(slitgeometry);
2249 slitgeometry = NULL;
2250
2251 giraffe_table_delete(grating);
2252 grating = NULL;
2253
2254 giraffe_table_delete(fibers);
2255 fibers = NULL;
2256
2257 return 1;
2258 }
2259
2260 cpl_frameset_insert(set, rimg_frame);
2261
2262 }
2263
2264 /* Error cube */
2265
2266 if (fov->cubes.errors != NULL) {
2267
2268 cxint component = 1;
2269
2270 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes;
2271
2272
2273 properties = giraffe_image_get_properties(rebinning->errors);
2274 properties = cpl_propertylist_duplicate(properties);
2275
2276 giraffe_add_frameset_info(properties, set, info.sequence);
2277
2278 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE_ERRORS,
2279 CPL_FRAME_LEVEL_FINAL,
2280 properties,
2281 fov,
2282 &component,
2283 creator);
2284
2285 cpl_propertylist_delete(properties);
2286 properties = NULL;
2287
2288 if (rimg_frame == NULL) {
2289 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2290
2291 giraffe_fov_delete(fov);
2292 fov = NULL;
2293
2294 giraffe_rebinning_destroy(rebinning);
2295 rebinning = NULL;
2296
2297 giraffe_table_delete(wcalcoeff);
2298 wcalcoeff = NULL;
2299
2300 giraffe_table_delete(slitgeometry);
2301 slitgeometry = NULL;
2302
2303 giraffe_table_delete(grating);
2304 grating = NULL;
2305
2306 giraffe_table_delete(fibers);
2307 fibers = NULL;
2308
2309 return 1;
2310 }
2311
2312 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2313
2314 if (status != 0) {
2315 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2316 "file '%s'! Aborting ...",
2317 cpl_frame_get_filename(rimg_frame));
2318
2319 cpl_frame_delete(rimg_frame);
2320
2321 giraffe_fov_delete(fov);
2322 fov = NULL;
2323
2324 giraffe_rebinning_destroy(rebinning);
2325 rebinning = NULL;
2326
2327 giraffe_table_delete(wcalcoeff);
2328 wcalcoeff = NULL;
2329
2330 giraffe_table_delete(slitgeometry);
2331 slitgeometry = NULL;
2332
2333 giraffe_table_delete(grating);
2334 grating = NULL;
2335
2336 giraffe_table_delete(fibers);
2337 fibers = NULL;
2338
2339 return 1;
2340 }
2341
2342 cpl_frameset_insert(set, rimg_frame);
2343 }
2344
2345 }
2346 else {
2347
2348 /* Data Cube (ESO 3D format) */
2349
2350 GiFrameCreator creator = (GiFrameCreator) giraffe_fov_save_cubes_eso3d;
2351
2352 properties = giraffe_image_get_properties(rebinning->spectra);
2353 properties = cpl_propertylist_duplicate(properties);
2354
2355 giraffe_add_frameset_info(properties, set, info.sequence);
2356
2357 rimg_frame = giraffe_frame_create(GIFRAME_SCIENCE_CUBE,
2358 CPL_FRAME_LEVEL_FINAL,
2359 properties,
2360 fov,
2361 NULL,
2362 creator);
2363
2364 cpl_propertylist_delete(properties);
2365 properties = NULL;
2366
2367 if (rimg_frame == NULL) {
2368 cpl_msg_error(_id, "Cannot create local file! Aborting ...");
2369
2370 giraffe_fov_delete(fov);
2371 fov = NULL;
2372
2373 giraffe_rebinning_destroy(rebinning);
2374 rebinning = NULL;
2375
2376 giraffe_table_delete(wcalcoeff);
2377 wcalcoeff = NULL;
2378
2379 giraffe_table_delete(slitgeometry);
2380 slitgeometry = NULL;
2381
2382 giraffe_table_delete(grating);
2383 grating = NULL;
2384
2385 giraffe_table_delete(fibers);
2386 fibers = NULL;
2387
2388 return 1;
2389 }
2390
2391 status = giraffe_fiberlist_attach(rimg_frame, fibers);
2392
2393 if (status != 0) {
2394 cpl_msg_error(_id, "Cannot attach fiber setup to local "
2395 "file '%s'! Aborting ...",
2396 cpl_frame_get_filename(rimg_frame));
2397
2398 cpl_frame_delete(rimg_frame);
2399
2400 giraffe_fov_delete(fov);
2401 fov = NULL;
2402
2403 giraffe_rebinning_destroy(rebinning);
2404 rebinning = NULL;
2405
2406 giraffe_table_delete(wcalcoeff);
2407 wcalcoeff = NULL;
2408
2409 giraffe_table_delete(slitgeometry);
2410 slitgeometry = NULL;
2411
2412 giraffe_table_delete(grating);
2413 grating = NULL;
2414
2415 giraffe_table_delete(fibers);
2416 fibers = NULL;
2417
2418 return 1;
2419 }
2420
2421 cpl_frameset_insert(set, rimg_frame);
2422
2423 }
2424
2425 giraffe_fov_delete(fov);
2426 fov = NULL;
2427
2428 }
2429
2430
2431 /*
2432 * Cleanup
2433 */
2434
2435 giraffe_table_delete(wcalcoeff);
2436
2437 giraffe_table_delete(slitgeometry);
2438 giraffe_table_delete(grating);
2439 giraffe_table_delete(fibers);
2440
2441 giraffe_rebinning_destroy(rebinning);
2442
2443 return 0;
2444
2445}
2446
2447
2448/*
2449 * Build table of contents, i.e. the list of available plugins, for
2450 * this module. This function is exported.
2451 */
2452
2453int
2454cpl_plugin_get_info(cpl_pluginlist* list)
2455{
2456
2457 cpl_recipe* recipe = cx_calloc(1, sizeof *recipe);
2458 cpl_plugin* plugin = &recipe->interface;
2459
2460
2461 cpl_plugin_init(plugin,
2462 CPL_PLUGIN_API,
2463 GIRAFFE_BINARY_VERSION,
2464 CPL_PLUGIN_TYPE_RECIPE,
2465 "giscience",
2466 "Process a science observation.",
2467 "For detailed information please refer to the "
2468 "GIRAFFE pipeline user manual.\nIt is available at "
2469 "http://www.eso.org/pipelines.",
2470 "Giraffe Pipeline",
2471 PACKAGE_BUGREPORT,
2473 giscience_create,
2474 giscience_exec,
2475 giscience_destroy);
2476
2477 cpl_pluginlist_append(list, plugin);
2478
2479 return 0;
2480
2481}
2482
2483
2484/* Structure of a lookup table entry for the LUT used to get values for
2485 * SPEC_RES. */
2486typedef struct _giraffe_lut_entry {
2487 const char* expmode;
2488 double specres;
2489 double lamrms; /* given in (px), to convert to (nm) one needs:
2490 lamrms * spec_length / 4100 */
2491 double spec_length;
2492 int lamnlin;
2493} giraffe_lut_entry;
2494
2495
2496#ifndef NDEBUG
2497
2502static cpl_boolean _giraffe_lut_is_sorted(const giraffe_lut_entry* lut,
2503 size_t nentries)
2504{
2505 size_t i;
2506 if (nentries < 2) return CPL_TRUE;
2507 for (i = 0; i < nentries - 1; ++i) {
2508 if (strcmp(lut[i].expmode, lut[i+1].expmode) >= 0) {
2509 return CPL_FALSE;
2510 }
2511 }
2512 return CPL_TRUE;
2513}
2514
2515#endif /* NDEBUG */
2516
2517
2525static const giraffe_lut_entry* _giraffe_find_lut_entry(const char* expmode)
2526{
2527 static giraffe_lut_entry lut[] = {
2528 /* INS_EXP_MODE lambda LAMRMS spec_length LAMNLIN
2529 * R = ------------- (px) (nm) line count
2530 * delta(lambda)
2531 */
2532 {"H379.", 25000, 0.2250, 20.0, 60},
2533 {"H379.0", 25000, 0.2250, 20.0, 60},
2534 {"H395.8", 22000, 0.1913, 21.1, 53},
2535 {"H412.4", 30000, 0.1326, 22.3, 48},
2536 {"H429.7", 23000, 0.1471, 23.5, 67},
2537 {"H447.1", 20000, 0.0906, 24.9, 63},
2538 {"H447.1A", 20000, 0.0906, 24.9, 63},
2539 {"H447.1B", 31000, 0.1297, 23.5, 58},
2540 {"H465.6", 23000, 0.1573, 22.4, 57},
2541 {"H484.5", 19000, 0.1175, 23.5, 57},
2542 {"H484.5A", 19000, 0.1175, 23.5, 57},
2543 {"H484.5B", 33000, 0.0907, 24.6, 61},
2544 {"H504.8", 22000, 0.1726, 25.2, 56},
2545 {"H525.8", 17000, 0.1397, 25.8, 49},
2546 {"H525.8A", 17000, 0.1397, 25.8, 49},
2547 {"H525.8B", 29000, 0.2014, 26.4, 44},
2548 {"H548.8", 20000, 0.2389, 26.9, 51},
2549 {"H572.8", 27000, 0.1844, 27.5, 49},
2550 {"H599.3", 18000, 0.1683, 28.3, 57},
2551 {"H627.3", 24000, 0.1268, 29.0, 50},
2552 {"H651.5", 17000, 0.1185, 30.0, 42},
2553 {"H651.5A", 17000, 0.1185, 30.0, 42},
2554 {"H651.5B", 35000, 0.1253, 31.5, 37},
2555 {"H665.", 17000, 0.2076, 33.0, 45},
2556 {"H665.0", 17000, 0.2076, 33.0, 45},
2557 {"H679.7", 19000, 0.1621, 34.5, 51},
2558 {"H710.5", 25000, 0.1495, 36.0, 48},
2559 {"H737.", 16000, 0.1456, 37.5, 47},
2560 {"H737.0", 16000, 0.1456, 37.5, 47},
2561 {"H737.0A", 16000, 0.1456, 37.5, 47},
2562 {"H737.0B", 35000, 0.1147, 39.5, 40},
2563 {"H769.1", 19000, 0.2811, 41.8, 35},
2564 {"H805.3", 14000, 0.2662, 42.4, 39},
2565 {"H805.3A", 14000, 0.2662, 42.4, 39},
2566 {"H805.3B", 25000, 0.2342, 42.9, 28},
2567 {"H836.6", 16000, 0.2032, 43.3, 21},
2568 {"H836.6A", 16000, 0.2032, 43.3, 21},
2569 {"H836.6B", 34000, 0.1073, 43.7, 14},
2570 {"H875.7", 18000, 0.2026, 44.3, 29},
2571 {"H920.5", 12000, 0.1568, 44.9, 32},
2572 {"H920.5A", 12000, 0.1568, 44.9, 32},
2573 {"H920.5B", 24000, 0.2531, 45.9, 28},
2574 {"L385.7", 7500, 0.3358, 58.0, 43},
2575 {"L427.2", 6300, 0.2152, 61.1, 62},
2576 {"L479.7", 7500, 0.1554, 71.0, 61},
2577 {"L543.1", 5800, 0.2065, 82.1, 58},
2578 {"L614.2", 6600, 0.1803, 79.0, 51},
2579 {"L682.2", 8100, 0.1843, 74.0, 50},
2580 {"L773.4", 5400, 0.1617, 94.0, 44},
2581 {"L881.7", 6600, 0.1614, 119.0, 29}
2582 };
2583 static const size_t nentries = sizeof(lut) / sizeof(giraffe_lut_entry);
2584 int low = 0; /* Bottom of search region. */
2585 int high = (int)nentries - 1; /* Top of search region. */
2586
2587 assert(_giraffe_lut_is_sorted(lut, nentries));
2588 assert(expmode != NULL);
2589
2590 /* Perform a binary search for the entry. */
2591 do {
2592 int mid = (low + high) >> 1; /* Find mid point of search range. */
2593 int result = strcmp(expmode, lut[mid].expmode);
2594 if (result == 0) {
2595 return &lut[mid];
2596 } else if (result < 0) {
2597 high = mid - 1;
2598 } else {
2599 low = mid + 1;
2600 }
2601 } while (high >= low);
2602 return NULL;
2603}
2604
2611static double _giraffe_lookup_specres(const char* expmode)
2612{
2613 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2614 if (entry == NULL) return NAN;
2615 return entry->specres;
2616}
2617
2624static double _giraffe_lookup_lamrms(const char* expmode)
2625{
2626 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2627 if (entry == NULL) return NAN;
2628 if (isnan(entry->lamrms) || isnan(entry->spec_length)) return NAN;
2629 return entry->lamrms * entry->spec_length / 4100.;
2630}
2631
2638static double _giraffe_lookup_lamnlin(const char* expmode)
2639{
2640 const giraffe_lut_entry* entry = _giraffe_find_lut_entry(expmode);
2641 if (entry == NULL) return -1;
2642 return entry->lamnlin;
2643}
2644
2645
2656static cpl_type _giraffe_calc_wave_type(double crval2, double crpix2,
2657 double cdelt2, cpl_size naxis2)
2658{
2659 static const double errfrac = 0.02;
2660 static const double single_precision_digits = 7;
2661 double lo = (1.0 - crpix2) * cdelt2;
2662 double hi = ((double)naxis2 - crpix2) * cdelt2;
2663 double maxwave = crval2 + (hi > lo ? hi : lo);
2664 double binfrac = (maxwave != 0.0) ? fabs(cdelt2 / maxwave) : 0.0;
2665 if (binfrac * errfrac < pow(10, -single_precision_digits)) {
2666 return CPL_TYPE_DOUBLE;
2667 } else {
2668 return CPL_TYPE_FLOAT;
2669 }
2670}
2671
2672
2682static cpl_boolean _giraffe_ancillary_data_available(const char* filename,
2683 const GiTable* fibertable)
2684{
2685 cpl_table* tbl = giraffe_table_get(fibertable);
2686 cpl_size i;
2687 const char** spectypes = NULL;
2688
2689 assert(filename != NULL);
2690
2691 cpl_error_ensure(tbl != NULL, cpl_error_get_code(), return CPL_FALSE,
2692 "The fiber table is not available for '%s'.", filename);
2693
2694 spectypes = cpl_table_get_data_string_const(tbl, GIALIAS_COLUMN_TYPE);
2695 cpl_error_ensure(spectypes != NULL, cpl_error_get_code(), return CPL_FALSE,
2696 "Could not fetch the '%s' column from the fiber setup"
2697 " table in '%s'.", GIALIAS_COLUMN_TYPE, filename);
2698 /*
2699 * Step through the table and check for fiber types other than Medusa
2700 * fibers. Also the simultaneous calibration fibers are not considered
2701 * as ancillary spectra and are ignored.
2702 */
2703 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2704 if ((spectypes[i][0] != '\0') && (strcmp(spectypes[i], "M") != 0)) {
2705 return CPL_TRUE;
2706 }
2707 }
2708 return CPL_FALSE;
2709}
2710
2711
2731static cpl_error_code _giraffe_make_ancillary_file(cpl_frameset* allframes,
2732 const char* outputfile,
2733 const char* infilename,
2734 const GiImage* fluximage,
2735 const GiTable* fibertable)
2736{
2737 cpl_error_code error = CPL_ERROR_NONE;
2738 cxint retcode;
2739 cpl_frame* frame = NULL;
2740 cpl_image* srcimg = giraffe_image_get(fluximage);
2741 GiImage* image = NULL;
2742 GiTable* table = giraffe_table_duplicate(fibertable);
2743 cpl_image* img = NULL;
2744 cpl_table* tbl = giraffe_table_get(table);
2745 cpl_image* subimg = NULL;
2746 cpl_propertylist* comments = NULL;
2747 cpl_size ny, i;
2748 int* indices = NULL;
2749 const char** spectypes = NULL;
2750
2751 assert(allframes != NULL);
2752 assert(outputfile != NULL);
2753 assert(infilename != NULL);
2754
2755 cpl_error_ensure(srcimg != NULL && table != NULL && tbl != NULL,
2756 cpl_error_get_code(), goto cleanup,
2757 "The image or table are not available for '%s'.",
2758 infilename);
2759
2760 /* Setup a new frame for the output file. */
2761 frame = cpl_frame_new();
2762 error |= cpl_frame_set_filename(frame, outputfile);
2763 error |= cpl_frame_set_tag(frame, GIALIAS_ASSO_PROCATG_VALUE);
2764 error |= cpl_frame_set_type(frame, CPL_FRAME_TYPE_IMAGE);
2765 error |= cpl_frame_set_group(frame, CPL_FRAME_GROUP_PRODUCT);
2766 error |= cpl_frame_set_level(frame, CPL_FRAME_LEVEL_FINAL);
2767 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2768 "Failed to setup a new output frame for '%s'.",
2769 outputfile);
2770
2771 /* First step to filter out the science entries in the image and fiber setup
2772 * table is to go through the table entries, mark the entries to remove, and
2773 * delete the ones that are marked. i.e. unselect everything, select all
2774 * non-science spectra, ignoring the simultaneous calibration spectra,
2775 * invert the selection and remove everything that remains marked as
2776 * selected. */
2777 error |= cpl_table_unselect_all(tbl);
2778 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2779 "Failed to unselect all entries in fiber setup table from"
2780 " '%s'.", infilename);
2781 cpl_table_or_selected_string(tbl, GIALIAS_COLUMN_TYPE, CPL_NOT_EQUAL_TO,
2782 "M");
2783 cpl_table_and_selected_int(tbl, GIALIAS_COLUMN_RP, CPL_NOT_EQUAL_TO, -1);
2784 cpl_table_not_selected(tbl);
2785 error |= cpl_table_erase_selected(tbl);
2786 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2787 "Failed to erase selected entries in fiber setup table"
2788 " from '%s'.", infilename);
2789
2790 /* Create a new output image which is wide enough to store the data with the
2791 * stripped out spectra removed. */
2792 ny = cpl_image_get_size_y(srcimg);
2793 image = giraffe_image_create(cpl_image_get_type(srcimg),
2794 cpl_table_get_nrow(tbl), ny);
2795 img = giraffe_image_get(image);
2797 image, giraffe_image_get_properties(fluximage));
2798 cpl_error_ensure(image != NULL && img != NULL && retcode == 0,
2799 cpl_error_get_code(), goto cleanup,
2800 "Failed to create image for output file '%s'.",
2801 outputfile);
2802
2803 error |= cpl_propertylist_update_string(giraffe_image_get_properties(image),
2804 GIALIAS_PROCATG,
2805 GIALIAS_ASSO_PROCATG_VALUE);
2806 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2807 "Could not update keyword '%s' for output file '%s'.",
2808 GIALIAS_PROCATG, outputfile);
2809
2810
2811 error |= cpl_propertylist_update_string(giraffe_image_get_properties(image),
2812 GIALIAS_PRODCATG,
2813 GIALIAS_PRODCATG_MOSSKY);
2814 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2815 "Could not update keyword '%s' for output file '%s'.",
2816 GIALIAS_PRODCATG, outputfile);
2817
2818 /* Strip out extra comments which will be added by CPL anyway. */
2819 if (cpl_propertylist_has(giraffe_image_get_properties(image), "COMMENT")) {
2820 cpl_size ic;
2821 const char* comments_to_remove[] = {
2822 " FITS (Flexible Image Transport System) format is defined in"
2823 " 'Astronomy",
2824 " and Astrophysics', volume 376, page 359; bibcode: 2001A&A..."
2825 "376..359H",
2826 NULL
2827 };
2828 cpl_propertylist* props = giraffe_image_get_properties(image);
2829 comments = cpl_propertylist_new();
2830 error |= cpl_propertylist_copy_property_regexp(comments, props,
2831 "^COMMENT$", 0);
2832 cpl_propertylist_erase_regexp(props, "^COMMENT$", 0);
2833 for (ic = 0; ic < cpl_propertylist_get_size(comments); ++ic) {
2834 const char** cmnt_str;
2835 cpl_property* p = cpl_propertylist_get(comments, ic);
2836 for (cmnt_str = comments_to_remove; *cmnt_str != NULL; ++cmnt_str) {
2837 if (strcmp(cpl_property_get_string(p), *cmnt_str) == 0) {
2838 goto dont_add_comment;
2839 }
2840 }
2841 /* Add back comments that should not be removed. */
2842 error |= cpl_propertylist_append_property(props, p);
2843 dont_add_comment:
2844 /* Land up here if the comment was found in the comments_to_remove
2845 * list of strings. */
2846 ;
2847 }
2848 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2849 "Failed to cleanup comments in primary HDU for '%s'.",
2850 outputfile);
2851 cpl_propertylist_delete(comments);
2852 comments = NULL;
2853 }
2854
2855 /* We now have to relabel the index numbers in the fiber setup table and
2856 * copy corresponding image columns to the new image. */
2857 indices = cpl_table_get_data_int(tbl, GIALIAS_COLUMN_INDEX);
2858 cpl_error_ensure(indices != NULL, cpl_error_get_code(), goto cleanup,
2859 "Could not fetch the '%s' column from the fiber setup"
2860 " table in '%s'.", GIALIAS_COLUMN_INDEX, infilename);
2861 for (i = 0; i < cpl_table_get_nrow(tbl); ++i) {
2862 cpl_size oldindex = indices[i];
2863 cpl_size newindex = i+1;
2864 indices[i] = newindex;
2865 subimg = cpl_image_extract(srcimg, oldindex, 1, oldindex, ny);
2866 cpl_error_ensure(subimg != NULL, cpl_error_get_code(), goto cleanup,
2867 "Could not extract sub image from '%s' at column %"
2868 CPL_SIZE_FORMAT".", infilename, oldindex);
2869 error |= cpl_image_copy(img, subimg, newindex, 1);
2870 cpl_image_delete(subimg);
2871 subimg = NULL;
2872 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2873 "Could write sub image from '%s' at column %"
2874 CPL_SIZE_FORMAT" to new image in '%s' at column %"
2875 CPL_SIZE_FORMAT".", infilename, oldindex, outputfile,
2876 newindex);
2877 }
2878
2879 /* Now write the actual FITS file. */
2880 retcode = giraffe_image_save(image, outputfile);
2881 cpl_error_ensure(retcode == 0, cpl_error_get_code(), goto cleanup,
2882 "Failed to write image to file '%s'.", outputfile);
2883 retcode = giraffe_fiberlist_attach(frame, table);
2884 cpl_error_ensure(retcode == 0, cpl_error_get_code(), goto cleanup,
2885 "Failed to attach the fiber setup table to file '%s'.",
2886 outputfile);
2887
2888 /* Add the new frame to the output frame set for the ancillary file.
2889 * Note: this should be the last step so that we do not delete this frame
2890 * anymore once in the frame set. */
2891 error |= cpl_frameset_insert(allframes, frame);
2892 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
2893 "Could not add a new frame to the frame list for '%s'.",
2894 outputfile);
2895
2896 giraffe_image_delete(image);
2897 giraffe_table_delete(table);
2898 return CPL_ERROR_NONE;
2899
2900cleanup:
2901 /* Error handling. Note: NULL pointer checks done by delete functions. */
2902 cpl_image_delete(subimg);
2903 giraffe_image_delete(image);
2904 giraffe_table_delete(table);
2905 cpl_frame_delete(frame);
2906 cpl_propertylist_delete(comments);
2907 return cpl_error_get_code();
2908}
2909
2910
2917static char* _giraffe_calc_format_string(cpl_size maxfiles)
2918{
2919 double ndigits = 1.0;
2920 if (maxfiles > 1) {
2921 /* Figure out how many digits must be printed to support a index number
2922 * as large as 'maxfiles'. */
2923 ndigits = ceil(log10((double)maxfiles + 1.0));
2924 }
2925 return cpl_sprintf("science_spectrum_%%0%.0f"CPL_SIZE_FORMAT".fits",
2926 ndigits);
2927}
2928
2929
2946static cxint _giraffe_make_sdp_spectra(const cxchar* flux_filename,
2947 const cxchar* err_filename,
2948 cxint nassoc_keys,
2949 cpl_frameset* allframes,
2950 const cpl_parameterlist* parlist,
2951 const cxchar* recipe_id)
2952{
2953 cxint result_code = 1;
2954 cxint errorcode;
2955 cpl_error_code error = CPL_ERROR_NONE;
2956 cpl_errorstate prestate;
2957 const char* ancillary_filename = "science_ancillary.fits";
2958 GiImage* fluximage = giraffe_image_new(CPL_TYPE_DOUBLE);
2959 GiImage* errimage = giraffe_image_new(CPL_TYPE_DOUBLE);
2960 GiTable* fibertable = NULL;
2961 const cxchar* fibertable_name = NULL;
2962 irplib_sdp_spectrum* spectrum = NULL;
2963 cpl_propertylist* extrakeys = cpl_propertylist_new();
2964 cpl_propertylist* tablekeys = cpl_propertylist_new();
2965 cpl_propertylist* props;
2966 char* pipe_id = cpl_sprintf("%s/%s", PACKAGE, VERSION);
2967 const char* dict_id = PRODUCT_DID;
2968 const cpl_frame* inherit = NULL;
2969 cpl_frameset* usedframes = NULL;
2970 cpl_frameset* rawframes = NULL;
2971 cpl_frameset_iterator* iterator = NULL;
2972 cpl_size nx, ny, i, filecount;
2973 double exptime = NAN;
2974 double mjdobs = NAN;
2975 double mjdend = NAN;
2976 double wavelmin = NAN;
2977 double wavelmax = NAN;
2978 double specbin = NAN;
2979 double crpix2 = NAN;
2980 double crval2 = NAN;
2981 double cdelt2 = NAN;
2982 const char* cunit2 = NULL;
2983 double specres;
2984 const char* expmode = NULL;
2985 char strbuf[64];
2986 const int* indices = NULL;
2987 const int* fps = NULL;
2988 const char** objects = NULL;
2989 const char** spectypes = NULL;
2990 const double* ras = NULL;
2991 const double* decs = NULL;
2992 const double* gcorr = NULL;
2993 const double* hcorr = NULL;
2994 const double* bcorr = NULL;
2995 char* formatstr = NULL;
2996 char* filename = NULL;
2997 cpl_type wavecoltype;
2998 cpl_array* refwavearray = NULL;
2999 cpl_array* array = NULL;
3000 float* data_float = NULL;
3001 double* data_double = NULL;
3002 cpl_vector* fluximgcol = NULL;
3003 cpl_vector* errimgcol = NULL;
3004 cpl_boolean got_ancillary_data = CPL_FALSE;
3005 cpl_size assoc_key_offset = 1;
3006 int lamnlin = -1;
3007 double lamrms = NAN;
3008 double specerr = NAN;
3009 double specsye = NAN;
3010 int obsid = -1;
3011 const char *dateobs = NULL;
3012
3013 cpl_error_ensure(flux_filename != NULL && err_filename != NULL
3014 && allframes != NULL && parlist != NULL
3015 && recipe_id != NULL, CPL_ERROR_NULL_INPUT, goto cleanup,
3016 "NULL input parameters.");
3017
3018 error |= cpl_propertylist_append_string(extrakeys, GIALIAS_PROCATG,
3019 GIALIAS_PROCATG_RBNSPEC_IDP);
3020 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_PROCATG,
3021 GIALIAS_PROCATG_COMMENT);
3022 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3023 "Could not set keyword '%s'.", GIALIAS_PROCATG);
3024
3025 /* Load the input flux and error data, including FITS header keywords. */
3026 errorcode = giraffe_image_load(fluximage, flux_filename, 0);
3027 cpl_error_ensure(errorcode == 0, cpl_error_get_code(), goto cleanup,
3028 "Could not load image data in primary HDU from '%s'.",
3029 flux_filename);
3030 errorcode = giraffe_image_load(errimage, err_filename, 0);
3031 cpl_error_ensure(errorcode == 0, cpl_error_get_code(), goto cleanup,
3032 "Could not load image data in primary HDU from '%s'.",
3033 err_filename);
3034
3035 giraffe_error_push();
3036 fibertable = giraffe_fiberlist_load(flux_filename, 1, GIALIAS_FIBER_SETUP);
3037 if (fibertable == NULL) {
3038 fibertable = giraffe_fiberlist_load(err_filename, 1,
3039 GIALIAS_FIBER_SETUP);
3040 fibertable_name = err_filename;
3041 } else {
3042 fibertable_name = flux_filename;
3043 }
3044 cpl_error_ensure(fibertable != NULL, CPL_ERROR_DATA_NOT_FOUND, goto cleanup,
3045 "Could not load the %s table from either '%s' or '%s'.",
3046 GIALIAS_FIBER_SETUP, flux_filename, err_filename);
3047 giraffe_error_pop();
3048
3049 /* Check that the image sizes are the same. */
3050 nx = cpl_image_get_size_x(giraffe_image_get(fluximage));
3051 ny = cpl_image_get_size_y(giraffe_image_get(fluximage));
3052 cpl_error_ensure(cpl_image_get_size_x(giraffe_image_get(errimage)) == nx
3053 && cpl_image_get_size_y(giraffe_image_get(errimage)) == ny,
3054 CPL_ERROR_INCOMPATIBLE_INPUT, goto cleanup,
3055 "The images in files '%s' and '%s' are not the same size.",
3056 flux_filename, err_filename);
3057
3058 /* Construct the used frame list from the existing list of all frames.
3059 * The frames to be included as the used frames are RAW and CALIB. */
3060 usedframes = cpl_frameset_new();
3061 rawframes = cpl_frameset_new();
3062 iterator = cpl_frameset_iterator_new(allframes);
3063 do {
3064 const cpl_frame* frame = cpl_frameset_iterator_get_const(iterator);
3065 if (frame != NULL) {
3066 switch (cpl_frame_get_group(frame)) {
3067 case CPL_FRAME_GROUP_RAW:
3068 /* Mark the first RAW frame from which to inherit keywords. */
3069 if (inherit == NULL) inherit = frame;
3070 error |= cpl_frameset_insert(rawframes,
3071 cpl_frame_duplicate(frame));
3072 error |= cpl_frameset_insert(usedframes,
3073 cpl_frame_duplicate(frame));
3074 break;
3075 case CPL_FRAME_GROUP_CALIB:
3076 error |= cpl_frameset_insert(usedframes,
3077 cpl_frame_duplicate(frame));
3078 break;
3079 default: /* Ignore all other groups */
3080 break;
3081 }
3082 }
3083 prestate = cpl_errorstate_get();
3084 error |= cpl_frameset_iterator_advance(iterator, 1);
3085 if (error == CPL_ERROR_ACCESS_OUT_OF_RANGE) {
3086 cpl_errorstate_set(prestate);
3087 break;
3088 } else if (error != CPL_ERROR_NONE) {
3089 goto cleanup;
3090 }
3091 } while (1);
3092
3093 cpl_error_ensure(inherit != NULL, CPL_ERROR_DATA_NOT_FOUND, goto cleanup,
3094 "No raw input frames found.");
3095
3096 /* Fetch the EXPTIME and MJD-OBS keywords from the product file. */
3097 props = giraffe_image_get_properties(fluximage);
3098 prestate = cpl_errorstate_get();
3099 exptime = cpl_propertylist_get_double(props, GIALIAS_EXPTIME);
3100 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3101 goto cleanup, "Could not find keyword '%s' in '%s'.",
3102 GIALIAS_EXPTIME, flux_filename);
3103 mjdobs = cpl_propertylist_get_double(props, GIALIAS_MJDOBS);
3104 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3105 goto cleanup, "Could not find keyword '%s' in '%s'.",
3106 GIALIAS_MJDOBS, flux_filename);
3107
3108 mjdend = mjdobs + exptime / 86400.;
3109
3110 /* Fetch the DATE-OBS and ESO OBS ID keywords from the product file. */
3111
3112 dateobs = cpl_propertylist_get_string(props, GIALIAS_DATEOBS);
3113 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3114 goto cleanup, "Could not find keyword '%s' in '%s'.",
3115 GIALIAS_DATEOBS, flux_filename);
3116
3117 obsid = cpl_propertylist_get_int(props, GIALIAS_OBSID);
3118 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3119 goto cleanup, "Could not find keyword '%s' in '%s'.",
3120 GIALIAS_OBSID, flux_filename);
3121
3122
3123 /* Calculate the min/max wavelength values. */
3124 crpix2 = cpl_propertylist_get_double(props, GIALIAS_CRPIX2);
3125 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3126 goto cleanup, "Could not find keyword '%s' in '%s'.",
3127 GIALIAS_CRPIX2, flux_filename);
3128 crval2 = cpl_propertylist_get_double(props, GIALIAS_CRVAL2);
3129 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3130 goto cleanup, "Could not find keyword '%s' in '%s'.",
3131 GIALIAS_CRVAL2, flux_filename);
3132 cdelt2 = cpl_propertylist_get_double(props, GIALIAS_CDELT2);
3133 cpl_error_ensure(cpl_errorstate_is_equal(prestate), cpl_error_get_code(),
3134 goto cleanup, "Could not find keyword '%s' in '%s'.",
3135 GIALIAS_CDELT2, flux_filename);
3136 cunit2 = cpl_propertylist_get_string(props, GIALIAS_CUNIT2);
3137 cpl_error_ensure(cunit2 != NULL, cpl_error_get_code(),
3138 goto cleanup, "Could not find keyword '%s' in '%s'.",
3139 GIALIAS_CUNIT2, flux_filename);
3140
3141 if (strcmp(cunit2, "nm") == 0) {
3142 wavelmin = (1.0 - crpix2) * cdelt2 + crval2;
3143 wavelmax = ((double)ny - crpix2) * cdelt2 + crval2;
3144 if (wavelmax < wavelmin) {
3145 double tmp = wavelmin;
3146 wavelmin = wavelmax;
3147 wavelmax = tmp;
3148 }
3149 specbin = fabs(cdelt2);
3150 } else {
3151 cpl_msg_warning(cpl_func, "Do not know how to handle keyword %s = '%s'."
3152 " Will not set WAVELMIN, WAVELMAX or SPEC_BIN.",
3153 GIALIAS_CUNIT2, cunit2);
3154 }
3155
3156 if (cpl_propertylist_has(props, GIALIAS_SETUPNAME)) {
3157 expmode = cpl_propertylist_get_string(props, GIALIAS_SETUPNAME);
3158 cpl_error_ensure(expmode != NULL, cpl_error_get_code(), goto cleanup,
3159 "Could not fetch the keyword '%s' from '%s'.",
3160 GIALIAS_SETUPNAME, flux_filename);
3161 } else if (cpl_propertylist_has(props, GIALIAS_GRATNAME)) {
3162 const char* name = cpl_propertylist_get_string(props, GIALIAS_GRATNAME);
3163 cpl_error_ensure(name != NULL, cpl_error_get_code(), goto cleanup,
3164 "Could not fetch the keyword '%s' from '%s'.",
3165 GIALIAS_GRATNAME, flux_filename);
3166 double wlen = cpl_propertylist_get_double(props, GIALIAS_GRATWLEN);
3167 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3168 cpl_error_get_code(), goto cleanup,
3169 "Could not find keyword '%s' in '%s'.",
3170 GIALIAS_GRATWLEN, flux_filename);
3171 strbuf[0] = name[0];
3172 char* numstr = cpl_sprintf("%.1f", wlen);
3173 strncpy(strbuf+1, numstr, sizeof(strbuf)-1);
3174 cpl_free(numstr);
3175 strbuf[sizeof(strbuf)-1] = '\0'; /* Ensure we have a NULL terminator. */
3176 expmode = strbuf;
3177 } else {
3178 cpl_error_set_message(cpl_func, CPL_ERROR_DATA_NOT_FOUND,
3179 "Neither '%s' nor '%s' and '%s' keywords were found in the"
3180 " file '%s'.", GIALIAS_SETUPNAME, GIALIAS_GRATNAME,
3181 GIALIAS_GRATWLEN, flux_filename);
3182 goto cleanup;
3183 }
3184
3185 specres = _giraffe_lookup_specres(expmode);
3186 if (isnan(specres)) {
3187 cpl_error_set_message(cpl_func, CPL_ERROR_ILLEGAL_INPUT,
3188 "The exposure mode '%s' is invalid or an unknown value."
3189 " Could not lookup the spectral resolution for 'SPEC_RES'.",
3190 expmode);
3191 goto cleanup;
3192 }
3193
3194 /* Add the FILTER keyword as OFILTER to the extra keywords list if it
3195 * exists. The FILTER keyword itself will be deleted. */
3196 if (cpl_propertylist_has(props, "FILTER")) {
3197 prestate = cpl_errorstate_get();
3198 cpl_propertylist_copy_property(extrakeys, props, "FILTER");
3199 cpl_property* prop = cpl_propertylist_get_property(extrakeys, "FILTER");
3200 cpl_property_set_name(prop, "OFILTER");
3201 cpl_error_ensure(cpl_errorstate_is_equal(prestate),
3202 cpl_error_get_code(), goto cleanup,
3203 "Could not rename the 'FILTER' keyword.");
3204 }
3205
3206 /* Write the ancillary data file if any ancillary data is available. */
3207 prestate = cpl_errorstate_get();
3208 got_ancillary_data = _giraffe_ancillary_data_available(flux_filename,
3209 fibertable);
3210 if (! cpl_errorstate_is_equal(prestate)) goto cleanup;
3211 if (got_ancillary_data) {
3212 error = _giraffe_make_ancillary_file(allframes, ancillary_filename,
3213 flux_filename, fluximage,
3214 fibertable);
3215 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3216 "Failed to write the ancillary file '%s'.",
3217 ancillary_filename);
3218 }
3219
3220 /* Create a new spectrum object and setup header keywords. */
3221 spectrum = irplib_sdp_spectrum_new();
3222 error = CPL_ERROR_NONE;
3223 error |= irplib_sdp_spectrum_set_origin(spectrum, GIALIAS_ORIGIN_VALUE);
3224 error |= irplib_sdp_spectrum_set_prodlvl(spectrum, GIALIAS_PRODLVL_VALUE);
3225 error |= irplib_sdp_spectrum_copy_dispelem(spectrum,
3226 props, GIALIAS_GRATNAME);
3227 error |= irplib_sdp_spectrum_set_specsys(spectrum, GIALIAS_SPECSYS_VALUE);
3228 error |= irplib_sdp_spectrum_set_extobj(spectrum, GIALIAS_EXT_OBJ_VALUE);
3229 /* The OBJECT, RA and DEC keywords we fill now with dummy values to maintain
3230 * the order of keywords. The actual values are set later. */
3231 error |= irplib_sdp_spectrum_set_object(spectrum, "");
3232 error |= irplib_sdp_spectrum_set_ra(spectrum, 0.0);
3233 error |= irplib_sdp_spectrum_set_dec(spectrum, 0.0);
3234 error |= irplib_sdp_spectrum_copy_exptime(spectrum, props, GIALIAS_EXPTIME);
3235 error |= irplib_sdp_spectrum_copy_texptime(spectrum,
3236 props, GIALIAS_EXPTIME);
3237 error |= irplib_sdp_spectrum_copy_mjdobs(spectrum, props, GIALIAS_MJDOBS);
3238 error |= irplib_sdp_spectrum_set_mjdend(spectrum, mjdend);
3239 if (cpl_propertylist_has(props, GIALIAS_TIMESYS)) {
3240 error |= irplib_sdp_spectrum_copy_timesys(spectrum,
3241 props, GIALIAS_TIMESYS);
3242 }
3243 error |= irplib_sdp_spectrum_copy_progid(spectrum, props, GIALIAS_PROGID);
3244 error |= irplib_sdp_spectrum_copy_obid(spectrum, 1, props, GIALIAS_OBSID);
3245 error |= irplib_sdp_spectrum_set_mepoch(spectrum, GIALIAS_M_EPOCH_VALUE);
3246 error |= irplib_sdp_spectrum_append_prov(spectrum, 1, rawframes);
3247 error |= irplib_sdp_spectrum_copy_procsoft(spectrum,
3248 props, GIALIAS_PROPIPEID);
3249 error |= irplib_sdp_spectrum_copy_obstech(spectrum, props, GIALIAS_PROTECH);
3250 error |= irplib_sdp_spectrum_set_prodcatg(spectrum, GIALIAS_PRODCATG_VALUE);
3251 error |= irplib_sdp_spectrum_set_fluxcal(spectrum, GIALIAS_FLUXCAL_VALUE);
3252 error |= irplib_sdp_spectrum_set_contnorm(spectrum, GIALIAS_CONTNORM_VALUE);
3253 /* Set dummy values for WAVELMIN, WAVELMAX and SPEC_BIN to keep the order
3254 * of the keywords. Will fill these in later with actual Heliocentric
3255 * corrected values. */
3256 error |= irplib_sdp_spectrum_set_wavelmin(spectrum, 0.0);
3257 error |= irplib_sdp_spectrum_set_wavelmax(spectrum, 0.0);
3258 error |= irplib_sdp_spectrum_set_specbin(spectrum, 0.0);
3259 error |= irplib_sdp_spectrum_set_totflux(spectrum, GIALIAS_TOTFLUX_VALUE);
3260 error |= irplib_sdp_spectrum_set_fluxerr(spectrum, GIALIAS_FLUXERR_VALUE);
3261 error |= irplib_sdp_spectrum_set_ncombine(spectrum,
3262 cpl_frameset_get_size(rawframes));
3263 error |= irplib_sdp_spectrum_set_referenc(spectrum, GIALIAS_REFERENC);
3264
3265 /* Set dummy value for SNR to maintain keyword ordering. Filled later. */
3266 error |= irplib_sdp_spectrum_set_snr(spectrum, 0.0);
3267
3268 /* Copy LAMNLIN if available from flux image else try look it up. */
3269 if (cpl_propertylist_has(props, GIALIAS_LAMNLIN)) {
3270 error |= irplib_sdp_spectrum_copy_lamnlin(spectrum, props,
3271 GIALIAS_LAMNLIN);
3272 lamnlin = irplib_sdp_spectrum_get_lamnlin(spectrum);
3273 } else {
3274 lamnlin = _giraffe_lookup_lamnlin(expmode);
3275 if (lamnlin != -1) {
3276 error |= irplib_sdp_spectrum_set_lamnlin(spectrum, lamnlin);
3277 }
3278 }
3279
3280 /* Copy LAMRMS if available from flux image else try look it up.
3281 * Note: we are going to have to correct this value later and fill it in
3282 * again for each spectrum. */
3283 if (cpl_propertylist_has(props, GIALIAS_LAMRMS)) {
3284 error |= irplib_sdp_spectrum_copy_lamrms(spectrum, props,
3285 GIALIAS_LAMRMS);
3286 lamrms = irplib_sdp_spectrum_get_lamrms(spectrum);
3287 } else {
3288 lamrms = _giraffe_lookup_lamrms(expmode);
3289 if (! isnan(lamrms)) {
3290 error |= irplib_sdp_spectrum_set_lamrms(spectrum, lamrms);
3291 }
3292 }
3293
3294 /* Copy SPEC_ERR if available from the flux image, else estimate it as:
3295 * if CRDER1 is available then
3296 * SPEC_ERR = CRDER1 / sqrt(LAMNLIN)
3297 * else
3298 * SPEC_ERR = LAMRMS / sqrt(LAMNLIN)
3299 * end
3300 *
3301 * Note: we are going to have to correct this value later and fill it in
3302 * again for each spectrum.
3303 */
3304 if (cpl_propertylist_has(props, GIALIAS_SPEC_ERR)) {
3305 error |= irplib_sdp_spectrum_copy_specerr(spectrum, props,
3306 GIALIAS_SPEC_ERR);
3307 specerr = irplib_sdp_spectrum_get_specerr(spectrum);
3308 } else if (lamnlin > 0) {
3309 if (cpl_propertylist_has(props, GIALIAS_CRDER1)) {
3310 prestate = cpl_errorstate_get();
3311 double crder1 = cpl_propertylist_get_double(props, GIALIAS_CRDER1);
3312 if (cpl_errorstate_is_equal(prestate) && crder1 > 0) {
3313 specerr = crder1 / sqrt(lamnlin);
3314 } else {
3315 error = cpl_error_get_code();
3316 }
3317 } else if (! isnan(lamrms)) {
3318 specerr = lamrms / sqrt(lamnlin);
3319 }
3320 if (! isnan(specerr)) {
3321 error |= irplib_sdp_spectrum_set_specerr(spectrum, specerr);
3322 }
3323 }
3324
3325 /* Copy SPEC_SYE if available from the flux image, else estimate it as:
3326 * 0.002 nm
3327 */
3328 if (cpl_propertylist_has(props, GIALIAS_SPEC_SYE)) {
3329 error |= irplib_sdp_spectrum_copy_specsye(spectrum, props,
3330 GIALIAS_SPEC_SYE);
3331 specsye = irplib_sdp_spectrum_get_specsye(spectrum);
3332 } else {
3333 /* Don't set the local specsye variable so that it does not get
3334 * corrected later. We want it to always be 0.002 nm. Just set the
3335 * keyword in the spectrum object directly. */
3336 error |= irplib_sdp_spectrum_set_specsye(spectrum, 0.002);
3337 }
3338
3339 error |= irplib_sdp_spectrum_set_specres(spectrum, specres);
3340 error |= irplib_sdp_spectrum_copy_gain(spectrum, props, GIALIAS_CONAD);
3341 error |= irplib_sdp_spectrum_copy_detron(spectrum, props, GIALIAS_RON);
3342 if (got_ancillary_data) {
3343 error |= irplib_sdp_spectrum_set_asson(spectrum, 1, ancillary_filename);
3344 error |= irplib_sdp_spectrum_set_assoc(spectrum, 1,
3345 GIALIAS_ASSOC_VALUE);
3346 error |= irplib_sdp_spectrum_set_assom(spectrum, 1, "");
3347 assoc_key_offset = 2;
3348 }
3349 for (i = assoc_key_offset; i < nassoc_keys + assoc_key_offset; ++i) {
3350 /* Add extra dummy association keywords if requested. */
3351 error |= irplib_sdp_spectrum_set_asson(spectrum, i, "");
3352 error |= irplib_sdp_spectrum_set_assoc(spectrum, i, "");
3353 error |= irplib_sdp_spectrum_set_assom(spectrum, i, "");
3354 }
3355
3356 error |= irplib_sdp_spectrum_set_voclass(spectrum, GIALIAS_VOCLASS_VALUE);
3357 error |= irplib_sdp_spectrum_set_vopub(spectrum, GIALIAS_VOPUB_VALUE);
3358 error |= irplib_sdp_spectrum_set_title(spectrum, ""); /* Set dummy value */
3359 error |= cpl_propertylist_append_double(tablekeys, GIALIAS_APERTURE,
3360 GIALIAS_APERTURE_VALUE);
3361 error |= cpl_propertylist_set_comment(tablekeys, GIALIAS_APERTURE,
3362 GIALIAS_APERTURE_COMMENT);
3363 /*
3364 * Normally: telapse = (mjdend - mjdobs) * 86400.
3365 * However, doing this calculation directly leads to rounding errors that
3366 * can cause the invalid condition TELAPSE < EXPTIME. Since we have:
3367 * mjdend = mjdobs + exptime / 86400.
3368 * we can simplify the above to be: telapse = exptime
3369 * which will always satisfy the condition TELAPSE >= EXPTIME.
3370 */
3371 error |= irplib_sdp_spectrum_set_telapse(spectrum, exptime);
3372 error |= irplib_sdp_spectrum_set_tmid(spectrum, (mjdobs + mjdend) * 0.5);
3373 /* Set dummy values for the SPEC_VAL, SPEC_BW, TDMIN and TDMAX values to
3374 * keep the order of the keywords on the header. Will fill these in later
3375 * with Heliocentric corrected values. */
3376 error |= irplib_sdp_spectrum_set_specval(spectrum, 0.0);
3377 error |= irplib_sdp_spectrum_set_specbw(spectrum, 0.0);
3378 error |= irplib_sdp_spectrum_set_nelem(spectrum, ny);
3379 error |= irplib_sdp_spectrum_set_tdmin(spectrum, 0.0);
3380 error |= irplib_sdp_spectrum_set_tdmax(spectrum, 0.0);
3381
3382 /* Add the keyword FPS */
3383 error |= cpl_propertylist_append_int(extrakeys, GIALIAS_FPS, -1);
3384 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_FPS,
3385 GIALIAS_FPS_COMMENT);
3386
3387 /* Add dummy [G,H,B]CORR keywords to be updated from the fiber table. */
3388 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_GEOCORR, NAN);
3389 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_GEOCORR,
3390 GIALIAS_GEOCORR_COMMENT);
3391 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_HELICORR, NAN);
3392 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_HELICORR,
3393 GIALIAS_HELICORR_COMMENT);
3394 error |= cpl_propertylist_append_double(extrakeys, GIALIAS_BARYCORR, NAN);
3395 error |= cpl_propertylist_set_comment(extrakeys, GIALIAS_BARYCORR,
3396 GIALIAS_BARYCORR_COMMENT);
3397
3398 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3399 "Could not setup the common SDP spectrum keywords.");
3400
3401 for (int qci = 0; qci < sizeof(sciqcpar) / sizeof(sciqcpar[0]); qci++) {
3402 if (cpl_propertylist_has(props, sciqcpar[qci])) {
3403 cpl_propertylist_copy_property(extrakeys, props, sciqcpar[qci]);
3404 }
3405 }
3406
3407 /* Figure out the data type required for the WAVE column to preserve the
3408 * precision of the data values. */
3409 wavecoltype = _giraffe_calc_wave_type(crval2, crpix2, cdelt2, ny);
3410
3411 /* Calculate the reference wavelength values (before corrections). */
3412 refwavearray = cpl_array_new(ny, CPL_TYPE_DOUBLE);
3413 data_double = cpl_array_get_data_double(refwavearray);
3414 assert(data_double != NULL);
3415 for (i = 1; i <= ny; ++i) {
3416 data_double[i-1] = (i-crpix2) * cdelt2 + crval2;
3417 }
3418 data_double = NULL;
3419
3420 /* Try setup the SDP table columns. */
3421 error |= irplib_sdp_spectrum_add_column(
3422 spectrum, GIALIAS_COLUMN_WAVE, wavecoltype,
3423 GIALIAS_COLUMN_WAVE_UNIT, NULL, GIALIAS_COLUMN_WAVE_TUTYP,
3424 GIALIAS_COLUMN_WAVE_TUCD, NULL);
3425
3426 /* Replace default keyword comment of the just created column */
3427 error |= irplib_sdp_spectrum_replace_column_comment(
3428 spectrum, GIALIAS_COLUMN_WAVE, "TUCD", "Air wavelength");
3429
3430 error |= irplib_sdp_spectrum_set_column_tcomm(
3431 spectrum, GIALIAS_COLUMN_WAVE, GIALIAS_COLUMN_WAVE_TCOMM);
3432 error |= irplib_sdp_spectrum_add_column(
3433 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, CPL_TYPE_DOUBLE,
3434 GIALIAS_COLUMN_FLUX_REDUCED_UNIT, NULL,
3435 GIALIAS_COLUMN_FLUX_REDUCED_TUTYP,
3436 GIALIAS_COLUMN_FLUX_REDUCED_TUCD, NULL);
3437 error |= irplib_sdp_spectrum_set_column_tcomm(
3438 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, "");
3439 error |= irplib_sdp_spectrum_add_column(
3440 spectrum, GIALIAS_COLUMN_ERR_REDUCED, CPL_TYPE_DOUBLE,
3441 GIALIAS_COLUMN_ERR_REDUCED_UNIT, NULL,
3442 GIALIAS_COLUMN_ERR_REDUCED_TUTYP,
3443 GIALIAS_COLUMN_ERR_REDUCED_TUCD, NULL);
3444 error |= irplib_sdp_spectrum_set_column_tcomm(
3445 spectrum, GIALIAS_COLUMN_ERR_REDUCED, "");
3446 error |= irplib_sdp_spectrum_add_column(
3447 spectrum, GIALIAS_COLUMN_SNR, CPL_TYPE_DOUBLE,
3448 GIALIAS_COLUMN_SNR_UNIT, NULL, GIALIAS_COLUMN_SNR_TUTYP,
3449 GIALIAS_COLUMN_SNR_TUCD, NULL);
3450 error |= irplib_sdp_spectrum_set_column_tcomm(
3451 spectrum, GIALIAS_COLUMN_SNR, GIALIAS_COLUMN_SNR_TCOMM);
3452 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3453 "Could not setup the SDP spectrum columns.");
3454
3455 indices = cpl_table_get_data_int_const(giraffe_table_get(fibertable),
3456 GIALIAS_COLUMN_INDEX);
3457 fps = cpl_table_get_data_int_const(giraffe_table_get(fibertable),
3458 GIALIAS_FPS);
3459 objects = cpl_table_get_data_string_const(giraffe_table_get(fibertable),
3460 GIALIAS_COLUMN_OBJECT);
3461 spectypes = cpl_table_get_data_string_const(giraffe_table_get(fibertable),
3462 GIALIAS_COLUMN_TYPE);
3463 ras = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3464 GIALIAS_COLUMN_RA);
3465 decs = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3466 GIALIAS_COLUMN_DEC);
3467 gcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3468 GIALIAS_COLUMN_GCORR);
3469 hcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3470 GIALIAS_COLUMN_HCORR);
3471 bcorr = cpl_table_get_data_double_const(giraffe_table_get(fibertable),
3472 GIALIAS_COLUMN_BCORR);
3473 cpl_error_ensure(indices != NULL && fps != NULL && objects != NULL
3474 && spectypes != NULL && ras != NULL && decs != NULL
3475 && gcorr != NULL && hcorr != NULL && bcorr != NULL,
3476 cpl_error_get_code(), goto cleanup,
3477 "Could not fetch data from the fiber setup table in '%s'.",
3478 fibertable_name);
3479
3480 formatstr = _giraffe_calc_format_string(
3481 cpl_table_get_nrow(giraffe_table_get(fibertable)));
3482
3483 cpl_errorstate tempes = cpl_errorstate_get();
3484
3485 cpl_size maxx = -1;
3486 cpl_size maxy = -1;
3487 cpl_image * maxim = cpl_image_collapse_create(giraffe_image_get(fluximage),0);
3488 cpl_image_get_maxpos(maxim, &maxx, &maxy);
3489
3490 cpl_image_delete(maxim);
3491
3492 cpl_errorstate_set(tempes);
3493
3494 /* Write the individual spectrum files: */
3495 filecount = 0;
3496 for (i = 0; i < cpl_table_get_nrow(giraffe_table_get(fibertable)); ++i) {
3497 const double* wave_data;
3498 double* flux_data;
3499 double* err_data;
3500 cpl_size j;
3501 double snr = 0.0;
3502 /* Keywords to remove: */
3503 const char* remregexp = "^(CDELT[0-9]+|CD[0-9]+_[0-9]+|CRPIX[0-9]+"
3504 "|CRDER[0-9]+|CSYER[0-9]+|BUNIT|BSCALE|BZERO"
3505 "|BLANK|FILTER)$";
3506 cpl_size specindex = indices[i];
3507 double vela, velb, beta;
3508 double correction_factor = 1.0;
3509
3510 /* Skip non-science spectra. */
3511 if (strcmp(spectypes[i], "M") != 0) continue;
3512
3513 filename = cpl_sprintf(formatstr, ++filecount);
3514
3515 /* Calculate the Heliocentric correction factor to apply.
3516 * The gcorr and hcorr values are in km/s, so must be converted to m/s.
3517 */
3518 vela = gcorr[i] * 1e3;
3519 velb = hcorr[i] * 1e3;
3520 beta = (vela + velb) / CPL_PHYS_C;
3521 cpl_error_ensure(-1 <= beta && beta <= 1,
3522 CPL_ERROR_ILLEGAL_OUTPUT, goto cleanup,
3523 "The velocities GCORR = %g and HCORR = %g for spectrum"
3524 "%"CPL_SIZE_FORMAT" in file '%s' give invalid"
3525 " Heliocentric correction factor values.",
3526 gcorr[i], hcorr[i], specindex, flux_filename);
3527 correction_factor = sqrt((1.0 + beta) / (1.0 - beta));
3528
3529 /* Calculate and set corrected wavelength array, remembering to cast
3530 * to the appropriate type. */
3531 wave_data = cpl_array_get_data_double_const(refwavearray);
3532 if (wavecoltype == CPL_TYPE_FLOAT) {
3533 data_float = cpl_malloc(ny * sizeof(float));
3534 for (j = 0; j < ny; ++j) {
3535 data_float[j] = wave_data[j] * correction_factor;
3536 }
3537 array = cpl_array_wrap_float(data_float, ny);
3538 } else {
3539 data_double = cpl_malloc(ny * sizeof(double));
3540 for (j = 0; j < ny; ++j) {
3541 data_double[j] = wave_data[j] * correction_factor;
3542 }
3543 array = cpl_array_wrap_double(data_double, ny);
3544 }
3545 error |= irplib_sdp_spectrum_set_column_data(
3546 spectrum, GIALIAS_COLUMN_WAVE, array);
3547 cpl_array_unwrap(array);
3548 array = NULL;
3549
3550 fluximgcol = cpl_vector_new_from_image_column(
3551 giraffe_image_get(fluximage), specindex);
3552 flux_data = cpl_vector_get_data(fluximgcol);
3553 cpl_error_ensure(flux_data != NULL, cpl_error_get_code(), goto cleanup,
3554 "Unable to extract data in column %"CPL_SIZE_FORMAT
3555 " from image in file '%s'.", specindex, flux_filename);
3556 array = cpl_array_wrap_double(flux_data, ny);
3557
3558 if(i==maxx - 1){
3559 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG, 'Y');
3560 }
3561 else{
3562 cpl_propertylist_update_char(extrakeys, GIALIAS_QCBRIGHTFLG, 'N');
3563 }
3564
3565 double fluxmean = cpl_array_get_mean(array);
3566 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMEANRED, fluxmean);
3567 error |= irplib_sdp_spectrum_set_column_data(
3568 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, array);
3569 cpl_array_unwrap(array);
3570 array = NULL;
3571
3572 errimgcol = cpl_vector_new_from_image_column(
3573 giraffe_image_get(errimage), specindex);
3574 err_data = cpl_vector_get_data(errimgcol);
3575 cpl_error_ensure(err_data != NULL, cpl_error_get_code(), goto cleanup,
3576 "Unable to extract data in column %"CPL_SIZE_FORMAT
3577 " from image in file '%s'.", specindex, err_filename);
3578 array = cpl_array_wrap_double(err_data, ny);
3579 error |= irplib_sdp_spectrum_set_column_data(
3580 spectrum, GIALIAS_COLUMN_ERR_REDUCED, array);
3581 cpl_array_unwrap(array);
3582 array = NULL;
3583
3584 data_double = cpl_malloc(ny * sizeof(double));
3585 for (j = 0; j < ny; ++j) {
3586 data_double[j] = (err_data[j] != 0.0) ? flux_data[j] / err_data[j]
3587 : 0.0;
3588 }
3589 array = cpl_array_wrap_double(data_double, ny);
3590 snr = cpl_array_get_median(array);
3591 double snrmean = cpl_array_get_mean(array);
3592 cpl_propertylist_update_double(extrakeys, GIALIAS_QCSNR, snrmean);
3593 error |= irplib_sdp_spectrum_set_column_data(spectrum,
3594 GIALIAS_COLUMN_SNR, array);
3595 cpl_array_unwrap(array);
3596 array = NULL;
3597 cpl_free(data_double);
3598 data_double = NULL;
3599
3600 cpl_vector_delete(fluximgcol);
3601 fluximgcol = NULL;
3602 cpl_vector_delete(errimgcol);
3603 errimgcol = NULL;
3604
3605 double estmag = 0;
3606 if(cpl_table_has_column(giraffe_table_get(fibertable), "MAGNITUDE")){
3607 estmag = cpl_table_get_double(giraffe_table_get(fibertable), "MAGNITUDE", i, NULL);
3608 }
3609 cpl_propertylist_update_double(extrakeys, GIALIAS_QCMAG, estmag);
3610
3611 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3612 "Could not setup the SDP spectrum columns for '%s'.",
3613 filename);
3614
3615 error |= irplib_sdp_spectrum_set_object(spectrum, objects[i]);
3616
3617 char * tmp_string;
3618
3619 tmp_string = cpl_sprintf("%s_%d_%s",
3620 objects[i],
3621 obsid,
3622 dateobs
3623 );
3624
3625 replace_spaces_with_underscores(tmp_string);
3626
3627 error |= irplib_sdp_spectrum_set_title(spectrum, tmp_string);
3628
3629 cpl_free(tmp_string);
3630
3631 error |= irplib_sdp_spectrum_set_ra(spectrum, ras[i]);
3632 error |= irplib_sdp_spectrum_set_dec(spectrum, decs[i]);
3633 error |= irplib_sdp_spectrum_set_snr(spectrum, snr);
3634 error |= irplib_sdp_spectrum_set_column_tcomm(
3635 spectrum, GIALIAS_COLUMN_FLUX_REDUCED, flux_filename);
3636 error |= irplib_sdp_spectrum_set_column_tcomm(
3637 spectrum, GIALIAS_COLUMN_ERR_REDUCED, err_filename);
3638
3639 error |= cpl_propertylist_update_int(extrakeys, GIALIAS_FPS, fps[i]);
3640 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_GEOCORR,
3641 gcorr[i]);
3642 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_HELICORR,
3643 hcorr[i]);
3644 error |= cpl_propertylist_update_double(extrakeys, GIALIAS_BARYCORR,
3645 bcorr[i]);
3646
3647 /* Set corrected values that depend on wavelengths. */
3648 error |= irplib_sdp_spectrum_set_wavelmin(spectrum,
3649 wavelmin * correction_factor);
3650 error |= irplib_sdp_spectrum_set_wavelmax(spectrum,
3651 wavelmax * correction_factor);
3652 error |= irplib_sdp_spectrum_set_specval(spectrum,
3653 (wavelmax + wavelmin) * 0.5 * correction_factor);
3654 error |= irplib_sdp_spectrum_set_specbw(spectrum,
3655 (wavelmax - wavelmin) * correction_factor);
3656 error |= irplib_sdp_spectrum_set_tdmin(spectrum,
3657 wavelmin * correction_factor);
3658 error |= irplib_sdp_spectrum_set_tdmax(spectrum,
3659 wavelmax * correction_factor);
3660 error |= irplib_sdp_spectrum_set_specbin(spectrum,
3661 specbin * correction_factor);
3662 if (! isnan(lamrms)) {
3663 error |= irplib_sdp_spectrum_set_lamrms(spectrum,
3664 lamrms * correction_factor);
3665 }
3666 if (! isnan(specerr)) {
3667 error |= irplib_sdp_spectrum_set_specerr(spectrum,
3668 specerr * correction_factor);
3669 }
3670 if (! isnan(specsye)) {
3671 error |= irplib_sdp_spectrum_set_specsye(spectrum,
3672 specsye * correction_factor);
3673 }
3674
3675 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3676 "Could not setup the SDP spectrum keywords for '%s'.",
3677 filename);
3678
3679 error |= irplib_dfs_save_spectrum(allframes, NULL, parlist, usedframes,
3680 inherit, spectrum, recipe_id,
3681 extrakeys, tablekeys, remregexp,
3682 pipe_id, dict_id, filename);
3683 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3684 "Failed to save SDP spectrum %"CPL_SIZE_FORMAT
3685 " to file '%s'.", specindex, filename);
3686
3687 error |= irplib_fits_update_checksums(filename);
3688 cpl_error_ensure(! error, cpl_error_get_code(), goto cleanup,
3689 "Failed to save update checksums for file '%s'.",
3690 filename);
3691 cpl_free(filename);
3692 filename = NULL;
3693 }
3694
3695 if (filecount == 0) {
3696 cpl_msg_warning(cpl_func, "No science spectra found in '%s'."
3697 " No SDP spectra created.", flux_filename);
3698 }
3699
3700 result_code = 0; /* Indicate success. */
3701
3702cleanup:
3703 /* Cleanup objects and memory. Note: the delete functions already check for
3704 * NULL pointers. */
3705 cpl_vector_delete(fluximgcol);
3706 cpl_vector_delete(errimgcol);
3707 cpl_array_unwrap(array);
3708 cpl_array_delete(refwavearray);
3709 cpl_free(data_float);
3710 cpl_free(data_double);
3711 cpl_free(filename);
3712 cpl_free(formatstr);
3713 cpl_frameset_delete(usedframes);
3714 cpl_frameset_delete(rawframes);
3715 cpl_frameset_iterator_delete(iterator);
3716 cpl_free(pipe_id);
3717 cpl_propertylist_delete(tablekeys);
3718 cpl_propertylist_delete(extrakeys);
3719 giraffe_image_delete(fluximage);
3720 giraffe_image_delete(errimage);
3721 giraffe_table_delete(fibertable);
3722 irplib_sdp_spectrum_delete(spectrum);
3723 return result_code;
3724}
cxint giraffe_add_rvcorrection(GiTable *fibers, const GiImage *spectra)
Add the barycentric and heliocentric corrections to the given fiber setup.
Definition: giastrometry.c:68
GiBiasConfig * giraffe_bias_config_create(cpl_parameterlist *list)
Creates a setup structure for a bias removal task.
Definition: gibias.c:3438
void giraffe_bias_config_add(cpl_parameterlist *list)
Adds parameters for the bias removal.
Definition: gibias.c:3597
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:3106
void giraffe_bias_config_destroy(GiBiasConfig *config)
Destroys a bias removal setup structure.
Definition: gibias.c:3569
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:478
void giraffe_extract_config_add(cpl_parameterlist *list)
Adds parameters for the spectrum extraction.
Definition: giextract.c:3508
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:2479
GiExtractConfig * giraffe_extract_config_create(cpl_parameterlist *list)
Creates a setup structure for the spectrum extraction.
Definition: giextract.c:3404
void giraffe_extract_config_destroy(GiExtractConfig *config)
Destroys a spectrum extraction setup structure.
Definition: giextract.c:3478
GiTable * giraffe_fibers_setup(const cpl_frame *frame, const cpl_frame *reference)
Setup a fiber list.
Definition: gifibers.c:218
GiTable * giraffe_fiberlist_load(const cxchar *filename, cxint dataset, const cxchar *tag)
Load a fiber table from a file.
Definition: gifiberutils.c:753
cxint giraffe_fiberlist_compare(const GiTable *fibers, const GiTable *reference)
Compare two fiber lists.
Definition: gifiberutils.c:951
cxint giraffe_fiberlist_attach(cpl_frame *frame, GiTable *fibers)
Attach a fiber table to a frame.
Definition: gifiberutils.c:883
GiFlatConfig * giraffe_flat_config_create(cpl_parameterlist *list)
Creates a setup structure for the flat field correction.
Definition: giflat.c:302
void giraffe_flat_config_destroy(GiFlatConfig *config)
Destroys a flat field setup structure.
Definition: giflat.c:353
void giraffe_flat_config_add(cpl_parameterlist *list)
Adds parameters for the flat field correction.
Definition: giflat.c:376
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
GiFieldOfViewConfig * giraffe_fov_config_create(cpl_parameterlist *list)
Creates a setup structure for the field of view reconstruction.
Definition: gifov.c:2012
void giraffe_fov_config_destroy(GiFieldOfViewConfig *config)
Destroys a field of view setup structure.
Definition: gifov.c:2067
GiFieldOfView * giraffe_fov_new(void)
Create an empty container for the results of the field of view reconstruction.
Definition: gifov.c:1393
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:1673
void giraffe_fov_delete(GiFieldOfView *self)
Deallocate a field of view object and its contents.
Definition: gifov.c:1494
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:428
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:1530
void giraffe_fov_config_add(cpl_parameterlist *list)
Adds parameters for the image and data cube construction.
Definition: gifov.c:2089
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:237
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:393
cpl_frame * giraffe_get_slitgeometry(const cpl_frameset *set)
Get the slit geometry frame from a frame set.
Definition: giframe.c:779
cpl_image * giraffe_image_get(const GiImage *self)
Gets the image data.
Definition: giimage.c:218
cpl_propertylist * giraffe_image_get_properties(const GiImage *self)
Get the properties of an image.
Definition: giimage.c:282
void giraffe_image_delete(GiImage *self)
Destroys an image.
Definition: giimage.c:181
GiImage * giraffe_image_create(cpl_type type, cxint nx, cxint ny)
Creates an image container of a given type.
Definition: giimage.c:95
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
cxint giraffe_image_save(GiImage *self, const cxchar *filename)
Write a Giraffe image to a file.
Definition: giimage.c:570
GiImage * giraffe_image_new(cpl_type type)
Creates an empty image container.
Definition: giimage.c:65
cxint giraffe_image_set_properties(GiImage *self, cpl_propertylist *properties)
Attaches a property list to an image.
Definition: giimage.c:312
cxint giraffe_image_load(GiImage *self, const cxchar *filename, cxint position)
Gets image data and properties from a file.
Definition: giimage.c:536
void giraffe_rebin_config_destroy(GiRebinConfig *config)
Destroys a spectrum extraction setup structure.
Definition: girebinning.c:4925
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:4051
GiRebinConfig * giraffe_rebin_config_create(cpl_parameterlist *list)
Creates a setup structure for the rebinning.
Definition: girebinning.c:4825
GiRebinning * giraffe_rebinning_new(void)
Create an empty rebinning results container.
Definition: girebinning.c:4693
void giraffe_rebinning_destroy(GiRebinning *rebinning)
Destroys a rebinning results container and its contents.
Definition: girebinning.c:4787
void giraffe_rebin_config_add(cpl_parameterlist *list)
Adds parameters for the rebinning.
Definition: girebinning.c:4949
GiSGCalConfig * giraffe_sgcalibration_config_create(cpl_parameterlist *list)
Creates a setup structure for the slit geometry calibration.
cxint giraffe_compute_offsets(GiTable *fibers, const GiRebinning *rebinning, const GiTable *grating, const GiTable *mask, const GiSGCalConfig *config)
Compute wavelength offsets for a set of rebinned input spectrum.
void giraffe_sgcalibration_config_destroy(GiSGCalConfig *config)
Destroys a sgcalibration field setup structure.
void giraffe_sgcalibration_config_add(cpl_parameterlist *list)
Adds parameters for the sgcalibration correction computation.
GiTable * giraffe_slitgeometry_load(const GiTable *fibers, const cxchar *filename, cxint pos, const cxchar *tag)
Load the slit geometry information for a given fiber setup.
GiTable * giraffe_table_new(void)
Creates a new, empty Giraffe table.
Definition: gitable.c:85
GiTable * giraffe_table_duplicate(const GiTable *src)
Duplicate a Giraffe table.
Definition: gitable.c:176
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
void giraffe_table_delete(GiTable *self)
Destroys a Giraffe table.
Definition: gitable.c:154
cpl_table * giraffe_table_get(const GiTable *self)
Get the table data from a Giraffe table.
Definition: gitable.c:433
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:784
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:1106
const cxchar * giraffe_get_license(void)
Get the pipeline copyright and license.
Definition: giutils.c:420
GiInstrumentMode giraffe_get_mode(cpl_propertylist *properties)
Determines the instrument mode from a property list.
Definition: giutils.c:442
Slit geometry calibration configuration data structure.

This file is part of the GIRAFFE Pipeline Reference Manual 2.18.3.
Documentation copyright © 2002-2006 European Southern Observatory.
Generated on Fri May 23 2025 16:31:10 by doxygen 1.9.6 written by Dimitri van Heesch, © 1997-2004