File: flames_prepslitff.c

package info (click to toggle)
cpl-plugin-uves 6.1.3+dfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 23,128 kB
  • sloc: ansic: 171,056; sh: 4,359; python: 3,002; makefile: 1,322
file content (906 lines) | stat: -rw-r--r-- 39,066 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
/*===========================================================================
  Copyright (C) 2001 European Southern Observatory (ESO)
 
  This program is free software; you can redistribute it and/or 
  modify it under the terms of the GNU General Public License as 
  published by the Free Software Foundation; either version 2 of 
  the License, or (at your option) any later version.
 
  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
 
  You should have received a copy of the GNU General Public 
  License along with this program; if not, write to the Free 
  Software Foundation, Inc., 675 Massachusetss Ave, Cambridge, 
  MA 02139, USA.
 
  Corresponding concerning ESO-MIDAS should be addressed as follows:
  Internet e-mail: midas@eso.org
  Postal address: European Southern Observatory
  Data Management Division 
  Karl-Schwarzschild-Strasse 2
  D 85748 Garching bei Muenchen 
  GERMANY
  ===========================================================================*/
/* Program  : prepslitff.c                                                 */
/* Author   : G. Mulas  -  ITAL_FLAMES Consortium                          */
/* Date     :                                                              */
/*                                                                         */
/* Purpose  : Missing                                                      */
/*                                                                         */
/*                                                                         */
/* Input:  see interface                                                   */ 
/*                                                                      */
/* Output:                                                              */
/*                                                                         */
/* DRS Functions called:                                                   */
/* none                                                                    */ 
/*                                                                         */ 
/* Pseudocode:                                                             */
/* Missing                                                                 */ 
/*                                                                         */ 
/* Version  :                                                              */
/* Last modification date: 2002/08/05                                      */
/* Who     When        Why                Where                            */
/* AMo     02-08-05   Add header         header                            */
/*-------------------------------------------------------------------------*/

#ifdef HAVE_CONFIG_H
#  include <config.h>
#endif

#include <flames_readslit0.h>
#include <flames_readslit.h>
#include <flames_prepslitff.h>
#include <flames_getordpos.h>
#include <flames_readordpos.h>
#include <flames_freeordpos.h>
#include <flames_stripfitsext.h>

#include <flames_midas_def.h>
#include <flames_uves.h>
#include <flames_newmatrix.h>
#include <flames_writeslitff.h>
#include <flames_freeslitflats.h>
#include <uves_msg.h>

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <math.h>
#include <ctype.h>

#define ULMAX(a,b) ((uint32_t)(a) > (uint32_t)(b) ? (uint32_t)(a) : (uint32_t)(b))
#define ULMIN(a,b) ((uint32_t)(a) < (uint32_t)(b) ? (uint32_t)(a) : (uint32_t)(b))

static int 
yshiftcompare(const void *slit1, const void *slit2);

static flames_err 
prepslitff(allslitflats *slitflats, orderpos *ordpos, 
           double decentSNR);




/**
 @brief prepares and normalise slit flat field data

 @param SLITCAT input slit FF data set
 @param OUTCAT  ouput slit FF data set
 @param MYORDER fibre order table
 @param BASENAME prefix to be used for slit FF data filenames
 @param DECENTSNR How large must the SNR on a fibre be in a calibration frame, at a given
                  order and x, for that slice to be considered "good"?

 @doc  -read Input frames and parameters
       -sort the FF frames in order of increasing YSHIFT
       -allocate and fill structures with data and finally calls actual prepslitff()
       -do slit FF cross-normalisation, then write output to disk
       -free memory
 */

int flames_prepslitff(const cpl_frameset *SLITCAT, cpl_frameset **OUTCAT,
                      const char *MYORDER, const char *BASENAME, const double *DECENTSNR) {
    int fileid = 0;
    int actvals = 0;
    int status = 0;
    int entrynum = 0;
    int unit = 0;
    int null = 0;
    //char incat[CATREC_LEN+1];
    const cpl_frameset *incat;
    //char outcat[CATREC_LEN+1];
    cpl_frameset **outcat;
    char basename[CATREC_LEN + 1];char
    filename[CATREC_LEN + 1];char
    ordername[CATREC_LEN + 1];char
    identifier[CATREC_LEN + 1];int32_t
    iframe = 0;
    double decentsnr = 0;

    orderpos *ordpos = 0;
    allslitflats *slitflats = 0;

    //memset(incat, 0, CATREC_LEN+1);
    //memset(outcat, 0, CATREC_LEN+1);
    memset(basename, 0, CATREC_LEN + 1);
    memset(filename, 0, CATREC_LEN + 1);
    memset(ordername, 0, CATREC_LEN + 1);
    memset(identifier, 0, CATREC_LEN + 1);

    /* allocate memory for the structures */
    ordpos = (orderpos *) calloc(1, sizeof(orderpos));
    slitflats = (allslitflats *) calloc(1, sizeof(allslitflats));

    /* enter the MIDAS environment */
    SCSPRO("prepslitff");

    /* read the SLITCAT keyword to know the name of the catalog file
   containing the list of int32_t slit FF frames */
    if ((status = SCKGETC_fs(SLITCAT, 1, 79, &actvals, &incat)) != 0) {
        /* the keyword seems undefined, protest... */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* get the outcat keyword */
    if ((status = SCKGETC_fsp(OUTCAT, 1, CATREC_LEN, &actvals, &outcat)) != 0) {
        /* I could not get the outcat keyword: complain... */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* get the myorder keyword */
    if ((status = SCKGETC(MYORDER, 1, CATREC_LEN, &actvals, ordername)) != 0) {
        /* I could not get the outcat keyword: complain... */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* get the basename for the files to be written to disk */
    if ((status = SCKGETC(BASENAME, 1, CATREC_LEN, &actvals, filename)) != 0) {
        /* I could not get the basename keyword: complain... */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }
    /* strip filename of the .fits extension, if it has one */
    if ((status = stripfitsext(filename, basename)) != NOERR) {
        /* error stripping extension */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* initialise DECENTSNR from keyword */
    if (SCKRDD(DECENTSNR, 1, 1, &actvals, &decentsnr, &unit, &null) != 0) {
        /* problems reading DECENTSNR */
        SCTPUT("Error reading the minimum acceptable SNR");
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* first open the input catalog and count the FF frames present */
    slitflats->nflats = 0;
    entrynum = 0;
    do {
        if ((status = SCCGET(incat,0,filename,identifier,&entrynum)) != 0) {
            /* error getting catalog entry */
            free(ordpos);
            free(slitflats);
            return flames_midas_fail();
        }
        /* did I get a valid catalog entry? */
        if (filename[0] != ' ') {
            slitflats->nflats++;
        }
    } while (filename[0] != ' ');

    /* check that nflats>0, otherwise, well... */
    if (slitflats->nflats == 0) {
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* in order to initialise firstorder and lastorder in slitflats, I
   need to read in the dummy table, therefore get that first */
    entrynum = 0;
    if ((status = SCCGET(incat,0,filename,identifier, &entrynum)) != 0) {
        /* error getting catalog entry */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* try to open the first frame */
    if ((status = SCFOPN(filename, FLAMESDATATYPE,
                    0, F_IMA_TYPE, &fileid)) != 0) {
        /* I could not open the frame */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    if ((status = SCDRDC(fileid, "CHIPCHOICE", 1, 1, 1, &actvals,
                    &slitflats->chipchoice, &unit, &null)) != 0) {
        /* something went wrong in SCDRDI */
        free(ordpos);
        free(slitflats);
        return (status);
    }

    /* close the first frame */
    if ((status = SCFCLO(fileid)) != 0) {
        /* problems closing the sigma frame */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* go for ordpos */
    /* initialise the ordpos structure from the dummy table descriptors */
    if ((status = readordpos(ordername, ordpos)) != NOERR) {
        /* something went wrong in the initialisation */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* check whether frames and order chip choices match */
    if (ordpos->chipchoice != slitflats->chipchoice) {
        /* no, they don't match */
        SCTPUT("Error: chip mismatch between frames and order table");
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* copy firstorder, lastorder and tab_io_oshift from ordpos */
    slitflats->firstorder = ordpos->firstorder;
    slitflats->lastorder = ordpos->lastorder;
    slitflats->tab_io_oshift = ordpos->tab_io_oshift;

    uves_msg_debug(
                    "Shifts = %d %d %d\n", ordpos->firstorder, ordpos->lastorder, ordpos->tab_io_oshift);

    /* initialise slitflats from the first frame */
    if ((status = readslit0(slitflats, 0, filename)) != NOERR) {
        /* error reading frame */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* now run a loop to fetch the other FF frames */
    for (iframe = 1; iframe <= slitflats->nflats - 1; iframe++) {
        entrynum = (int) iframe;
        /* get filename */
        if ((status = SCCGET(incat,0,filename,identifier,&entrynum)) != 0) {
            /* error getting catalog entry */
            return flames_midas_fail();
        }
        /* read frame */
        if ((status = readslit(slitflats, iframe, filename)) != NOERR) {
            /* error reading frame */
            return flames_midas_fail();
        }
    }
    /* good, all FF frames have been read in */
    /* take care to sort the FF frames in order of increasing YSHIFT */
    qsort(slitflats->slit, (size_t) slitflats->nflats, sizeof(slitFF),
          yshiftcompare);

    /* now that the structures have been allocated and filled with data,
   call the actual prepslitff */
    uves_msg("snr=%f", decentsnr);
    //writeslitff(slitflats, basename, outcat);

    if ((status = prepslitff(slitflats, ordpos, decentsnr)) != NOERR) {
        /* something went wrong with cross normalisation */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* the actual cross-normalisation has been done, here begins
   the phase of writing it down to disk */

    /* write it all to disk */
    if ((status = writeslitff(slitflats, basename, outcat)) != NOERR) {
        /* something went wrong writing this stuff to disk */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }

    /* free the memory allocated for the structures */
    if ((status = freeordpos(ordpos)) != NOERR) {
        /* error freeing ordpos */
        free(ordpos);
        free(slitflats);
        return flames_midas_fail();
    }
    free(ordpos);
    if ((status = freeslitflats(slitflats)) != NOERR) {
        /* error freeing slitflats */
        return flames_midas_fail();
    }
    free(slitflats);

    return (SCSEPI());

}

static flames_err prepslitff(allslitflats *slitflats, orderpos *ordpos,
                             double decentSNR) {

    flames_err status;
    int32_t iframe, iorder, ix, iy, goodpixels;
    double order, x, ordercentre, framecentre, plow, phigh;
    frame_data numerator, denominator, numerator2, denominator2;
    frame_data numsigma, densigma, pixel, sigma;
    int *framelist, *toclear;
    int32_t i, current, topmost, nframes, oldnframes;
    double currcentre, prevcentre;
    frame_data normfactor;
    slitFF *newslit;
    frame_data **dataframe, **sigmaframe;
    frame_mask **badframe;
    frame_data decenthreshold, decentSNR2;
    slitFF *myslit = 0;
    slitFF *currslit = 0;
    slitFF *topslit = 0;

    slitFF *firstslit = 0;


    frame_data fdbuf1 = 0;
    frame_data slitpixel = 0;
    frame_data slitpixel2 = 0;
    frame_data *fdvecbuf1 = 0;
    frame_data *fdvecbuf2 = 0;
    frame_data *fdvecbuf3 = 0;
    frame_data *fdvecbuf4 = 0;
    frame_data *fdvecbuf5 = 0;
    frame_data *fdvecbuf6 = 0;
    frame_data *fdvecbuf7 = 0;
    frame_mask *fmvecbuf1 = 0;
    frame_mask *fmvecbuf2 = 0;
    frame_mask *fmvecbuf3 = 0;
    frame_mask *fmvecbuf4 = 0;
    int32_t *lvecbuf1 = 0;
    int32_t *lvecbuf2 = 0;
    int32_t *lvecbuf3 = 0;
    int32_t *lvecbuf4 = 0;
    int32_t *lvecbuf5 = 0;
    int32_t *lvecbuf6 = 0;
    int32_t *lvecbuf7 = 0;
    int32_t *lvecbuf8 = 0;
    int32_t iyixuplimit = 0;
    int32_t iyixindex = 0;
    int32_t iorderixoffset = 0;
    int32_t iorderixindex = 0;
    int32_t commbottom = 0;
    int32_t commtop = 0;

    /* since it happens to have almost null slit values on unmasked bad
   columns, try to avoid them */
    decenthreshold = (frame_data) decentSNR
                    * pow(slitflats->gain * slitflats->ron, .5);
    uves_msg("thresh=%f", decenthreshold);
    decentSNR2 = (frame_data) (decentSNR * decentSNR);

    iyixuplimit = (slitflats->subrows * slitflats->subcols) - 1;

    lvecbuf1 = slitflats->lowbound[0];
    lvecbuf2 = slitflats->highbound[0];
    lvecbuf3 = slitflats->slit[0].lowbound[0];
    lvecbuf4 = slitflats->slit[0].highbound[0];
    fmvecbuf1 = slitflats->goodx[0];
    fdvecbuf1 = slitflats->normfactor[0];
    fdvecbuf2 = slitflats->slit[0].data[0];
    fdvecbuf3 = slitflats->slit[0].sigma[0];
    fmvecbuf2 = slitflats->slit[0].badpixel[0];

    /* before beginning the actual work, check that the flat part the orders
   in each frame is at least 1 pixel wide */
    for (iframe = 0; iframe <= slitflats->nflats - 1; iframe++) {
        if (2 * slitflats->slit[iframe].halfwidth / slitflats->substepy < 1) {
            return (MAREMMA);
        }
        myslit = slitflats->slit + iframe;
        fdvecbuf4 = myslit->data[0];
        fdvecbuf5 = myslit->sigma[0];
        fmvecbuf3 = myslit->badpixel[0];
        for (iyixindex = 0; iyixindex <= iyixuplimit; iyixindex++) {
            if ((fmvecbuf3[iyixindex] == 0)
                            && (((fdbuf1 = fdvecbuf4[iyixindex]) < decenthreshold)
                                            || ((fdbuf1 * fdbuf1 / fdvecbuf5[iyixindex]) < decentSNR2))) {
                fmvecbuf3[iyixindex] = 1;
                /*
         uves_msg("ok1 rat1=%f check1=%f rat2=%f check2=%f",
         fdbuf1,decenthreshold,
         fdbuf1*fdbuf1/fdvecbuf5[iyixindex],decentSNR2);
                 */
            }
        }
    }

    /* begin looping over orders at first */
    for (iorder = 0; iorder <= ((ordpos->lastorder) - (ordpos->firstorder));
                    iorder++) {
        iorderixoffset = iorder * slitflats->subcols;
        order = (double) (iorder + (ordpos->firstorder));
        /* loop over x... */
        for (ix = 0; ix <= (slitflats->subcols - 1); ix++) {
            iorderixindex = iorderixoffset + ix;
            /* convert the ix pixel coordinate to the x world coordinate */
            x = slitflats->substartx + (slitflats->substepx) * ((double) ix);
            /* find the unshifted central position and slope of this
       order at this x */
            /* bail out if the function call return an error status */
            if ((status = get_ordpos(ordpos, order, x, &ordercentre)) != NOERR) {
                return (status);
            }
            /* loop over FF frames */
            for (iframe = 0; iframe <= slitflats->nflats - 1; iframe++) {
                /* compute the order boundaries for each frame in this order in
         pixel coordinates*/
                myslit = slitflats->slit + iframe;
                lvecbuf5 = myslit->lowbound[0];
                lvecbuf6 = myslit->highbound[0];
                framecentre = ordercentre + myslit->yshift;
                /* remember that each pixel has a finite size, its position is
         the position of its centre and we want to be conservative in
         setting these boundaries */
                plow = ceil(
                                (framecentre - myslit->halfwidth) / slitflats->substepy + 0.5);
                phigh = floor(
                                (framecentre + myslit->halfwidth) / slitflats->substepy - 0.5);
                /* check boundaries and truncate to integer appropriately */
                /* is the whole interval out of the boundaries? */
                if ((phigh < 0) || (plow > (double) (slitflats->subrows) - 1)) {
                    /* the y loop must be skipped */
                    lvecbuf5[iorderixindex] = 1;
                    lvecbuf6[iorderixindex] = 0;
                } else {
                    /* is the upper limit above the upper boundary? */
                    if (phigh >= (double) (slitflats->subrows - 1)) {
                        /* yes it is */
                        lvecbuf6[iorderixindex] = slitflats->subrows - 1;
                    } else {
                        /* no it is not, truncate the upper limit to integer */
                        lvecbuf6[iorderixindex] = (int32_t) phigh;
                    }
                    /* is the lower limit below the lower boundary? */
                    if (plow <= 0) {
                        /* yes it is */
                        lvecbuf5[iorderixindex] = 0;
                    } else {
                        /* no it is not, truncate the lower limit to integer */
                        lvecbuf5[iorderixindex] = (int32_t) plow;
                    }
                }
            }
            /* set the goodx mask to good by default */
            fmvecbuf1[iorderixindex] = 0;
            /* set the overall boundaries equal to the boudaries for the first
       frame, at first */
            lvecbuf1[iorderixindex] = lvecbuf3[iorderixindex];
            lvecbuf2[iorderixindex] = lvecbuf4[iorderixindex];
            /* now compute the overall illumination factors; we do this using
       the first frame, since all subsequent frames will be scaled to
       match this */
            goodpixels = 0;
            numerator = 0;
            for (iy = lvecbuf1[iorderixindex]; iy <= lvecbuf2[iorderixindex]; iy++) {
                iyixindex = (iy * slitflats->subcols) + ix;
                /* take out insanely valued pixels before they cause real damage */
                if (fdvecbuf2[iyixindex] < decenthreshold) {
                    fmvecbuf2[iyixindex] = 1;
                    /*
           uves_msg("ok2 rat1=%f check1=%f",
           fdvecbuf2[iyixindex],decenthreshold);
                     */
                    //uves_msg("ok2");
                }
                /* is this pixel good? */
                if (fmvecbuf2[iyixindex] == 0) {
                    /* yes, it is, add its contribution to the overall
           illumination factor */
                    goodpixels++;
                    numerator += fdvecbuf2[iyixindex];
                }
            }
            /* did I find any good pixels? */
            if (goodpixels > 0
                            && (normfactor = numerator / ((frame_data) goodpixels))
                            > decenthreshold)
                fdvecbuf1[iorderixindex] = normfactor;
            else
                fdvecbuf1[iorderixindex] = 0;
            /* now compute the relative normalisation factors, for each frame
       relative to the previous one; of course this is skipped in case
       we have just one int32_t slit FF frame */
            myslit = slitflats->slit;
            lvecbuf5 = myslit->lowbound[0];
            lvecbuf6 = myslit->highbound[0];
            fdvecbuf4 = myslit->data[0];
            fdvecbuf5 = myslit->sigma[0];
            fmvecbuf3 = myslit->badpixel[0];
            for (iframe = 1; iframe <= slitflats->nflats - 1; iframe++) {
                /* compare the overall boundaries so far with the boundaries of
         this frame */
                lvecbuf7 = lvecbuf5;
                lvecbuf8 = lvecbuf6;
                fdvecbuf6 = fdvecbuf4;
                fdvecbuf7 = fdvecbuf5;
                fmvecbuf4 = fmvecbuf3;
                myslit = slitflats->slit + iframe;
                fdvecbuf4 = myslit->data[0];
                fdvecbuf5 = myslit->sigma[0];
                fmvecbuf3 = myslit->badpixel[0];
                lvecbuf5 = myslit->lowbound[0];
                lvecbuf6 = myslit->highbound[0];
                if (lvecbuf1[iorderixindex] > lvecbuf5[iorderixindex])
                    lvecbuf1[iorderixindex] = lvecbuf5[iorderixindex];
                if (lvecbuf2[iorderixindex] < lvecbuf6[iorderixindex])
                    lvecbuf2[iorderixindex] = lvecbuf6[iorderixindex];
                numerator = 0;
                numsigma = 0;
                denominator = 0;
                densigma = 0;
                goodpixels = 0;
                /* loop over the common part of the slit in iframe and the
         preceding one */
                if (lvecbuf5[iorderixindex] > lvecbuf7[iorderixindex])
                    commbottom = lvecbuf5[iorderixindex];
                else
                    commbottom = lvecbuf7[iorderixindex];
                if (lvecbuf6[iorderixindex] < lvecbuf8[iorderixindex])
                    commtop = lvecbuf6[iorderixindex];
                else
                    commtop = lvecbuf8[iorderixindex];
                for (iy = commbottom; iy <= commtop; iy++) {
                    iyixindex = (iy * slitflats->subcols) + ix;
                    /* take out insanely valued pixels before they cause real damage */
                    if (fdvecbuf4[iyixindex] < decenthreshold)
                        fmvecbuf3[iyixindex] = 1;
                    /*
           uves_msg("ok3 rat1=%f check1=%f",
           fdvecbuf3[iyixindex],decenthreshold);
                     */
                    //uves_msg("ok3");
                    /* is this pixel good in both frames? */
                    if ((fmvecbuf3[iyixindex] == 0) && (fmvecbuf4[iyixindex] == 0)) {
                        /* yes it is, add its contribution to all normalisation factors */
                        goodpixels++;
                        numerator += fdvecbuf6[iyixindex];
                        numsigma += fdvecbuf7[iyixindex];
                        denominator += fdvecbuf4[iyixindex];
                        densigma += fdvecbuf5[iyixindex];
                    }
                }
                /* were any overlapping good pixels found? */
                if ((goodpixels != 0) && (denominator > FDEPSILON)) {
                    /* yes, therefore do normalise */
                    for (iy = lvecbuf5[iorderixindex]; iy <= lvecbuf6[iorderixindex];
                                    iy++) {
                        iyixindex = (iy * slitflats->subcols) + ix;
                        /* first compute the variance of the normalised pixel */
                        numerator2 = numerator * numerator;
                        denominator2 = denominator * denominator;
                        slitpixel = fdvecbuf4[iyixindex];
                        slitpixel2 = slitpixel * slitpixel;
                        fdvecbuf5[iyixindex] = fdvecbuf5[iyixindex] * numerator2
                                        / denominator2 + numsigma * slitpixel2 / denominator2
                                        + densigma * slitpixel2 * numerator2
                                        / (denominator2 * denominator2);
                        /* now compute the scaled pixel value */
                        fdvecbuf4[iyixindex] = numerator * fdvecbuf4[iyixindex]
                                                                     / denominator;
                    }
                } else {
                    /* no overlapping good pixels found, mark this goodx as bad */
                    fmvecbuf1[iorderixindex] = 1;
                }
            }
            /* now run over the overall interval and compute each pixel as a
       weighted average of the available values for that position */
            if (fmvecbuf1[iorderixindex] == 0) {
                for (iy = lvecbuf1[iorderixindex]; iy <= lvecbuf2[iorderixindex];
                                iy++) {
                    iyixindex = (iy * slitflats->subcols) + ix;
                    denominator = 0;
                    numerator = 0;
                    goodpixels = 0;
                    /* cycle through frames to see which ones include this pixel */
                    for (iframe = 0; iframe <= slitflats->nflats - 1; iframe++) {
                        myslit = slitflats->slit + iframe;
                        fdvecbuf4 = myslit->data[0];
                        fdvecbuf5 = myslit->sigma[0];
                        fmvecbuf3 = myslit->badpixel[0];
                        lvecbuf5 = myslit->lowbound[0];
                        lvecbuf6 = myslit->highbound[0];
                        if ((iy >= lvecbuf5[iorderixindex])
                                        && (iy <= lvecbuf6[iorderixindex])) {
                            /* if it is a good pixel in this frame, add it to the average */
                            if (fmvecbuf3[iyixindex] == 0) {
                                goodpixels++;
                                numerator += fdvecbuf4[iyixindex] / fdvecbuf5[iyixindex];
                                denominator += 1 / fdvecbuf5[iyixindex];
                            }
                        }
                    }
                    /* if an average could be computed, put it back in the frames */
                    if (goodpixels != 0) {
                        /* average pixel value */
                        pixel = (frame_data) (numerator / denominator);
                        /* sigma of the average pixel value */
                        sigma = (frame_data) (1 / denominator);
                        /* cycle through frames to see which ones include this pixel */
                        for (iframe = 0; iframe <= slitflats->nflats - 1; iframe++) {
                            myslit = slitflats->slit + iframe;
                            fdvecbuf4 = myslit->data[0];
                            fdvecbuf5 = myslit->sigma[0];
                            fmvecbuf3 = myslit->badpixel[0];
                            lvecbuf5 = myslit->lowbound[0];
                            lvecbuf6 = myslit->highbound[0];
                            if ((iy >= lvecbuf5[iorderixindex])
                                            && (iy <= lvecbuf6[iorderixindex])) {
                                /* this is a good pixel now */
                                fmvecbuf3[iyixindex] = 0;
                                fdvecbuf4[iyixindex] = pixel;
                                fdvecbuf5[iyixindex] = sigma;
                            }
                        }
                    }
                }
            }
        }
    }

    /* find the minimum set of int32_t slit frames that covers the whole interval */
    framelist = ivector(0, slitflats->nflats - 1);
    /* find the lowest starting */
    current = 0;
    currslit = slitflats->slit;
    for (i = 1; i <= slitflats->nflats - 1; i++) {
        myslit = slitflats->slit + i;
        if ((myslit->yshift - myslit->halfwidth)
                        < (currslit->yshift - currslit->halfwidth)) {
            current = i;
            currslit = myslit;
        }
    }
    framelist[0] = topmost = current;
    topslit = currslit;
    nframes = 1;
    do {
        oldnframes = nframes;
        /* find the overlapping frame with the highest upper limit */
        for (i = 0; i <= slitflats->nflats - 1; i++) {
            myslit = slitflats->slit + i;
            /* is the lower limit of the i frame sufficiently lower than the
       upper limit of the current frame (i.e. can it overlap the current
       frame?)? */
            if ((topslit->yshift + topslit->halfwidth)
                            - (myslit->yshift - myslit->halfwidth) > slitflats->substepy) {
                /* is the upper limit of the i frame higher than the upper limit of
         the current frame? */
                if ((myslit->yshift + myslit->halfwidth)
                                > (currslit->yshift + currslit->halfwidth)) {
                    current = i;
                    currslit = myslit;
                }
            }
        }
        /* did I find another frame? */
        if (current != topmost) {
            /* add it to the list */
            framelist[nframes] = topmost = current;
            topslit = currslit;
            nframes++;
        }
    } while (nframes != oldnframes);

    /* ok, now I have the list of necessary frames, prepare a new
   slit array and put just the necessary frames in it */
    newslit = (slitFF *) calloc((size_t) nframes, sizeof(slitFF));
    toclear = ivector(0, slitflats->nflats - 1);
    for (i = 0; i <= slitflats->nflats - 1; i++) {
        toclear[i] = 0;
    }
    /* fill newslit with the necessary frames */
    for (i = 0; i <= nframes - 1; i++) {
        slitFF* mynewslit = newslit + i;
        myslit = slitflats->slit + framelist[i];
        mynewslit->data = myslit->data;
        mynewslit->sigma = myslit->sigma;
        mynewslit->badpixel = myslit->badpixel;
        mynewslit->yshift = myslit->yshift;
        mynewslit->framename = myslit->framename;
        mynewslit->sigmaname = myslit->sigmaname;
        mynewslit->badname = myslit->badname;
        mynewslit->boundname = myslit->boundname;
        mynewslit->halfwidth = myslit->halfwidth;
        mynewslit->lowbound = myslit->lowbound;
        mynewslit->highbound = myslit->highbound;
        toclear[framelist[i]] = 1;
    }
    /* free unused frames */
    for (i = 0; i <= slitflats->nflats - 1; i++) {
        /* is this slit unused? */
        if (toclear[i] == 0) {
            myslit = slitflats->slit + i;
            free_fdmatrix(myslit->data, 0, slitflats->subrows, 0, slitflats->subcols);
            free_fdmatrix(myslit->sigma, 0, slitflats->subrows, 0,
                          slitflats->subcols);
            free_fmmatrix(myslit->badpixel, 0, slitflats->subrows, 0,
                          slitflats->subcols);
            free_lmatrix(myslit->lowbound, 0, ordpos->lastorder - ordpos->firstorder,
                         0, slitflats->subcols);
            free_lmatrix(myslit->highbound, 0, ordpos->lastorder - ordpos->firstorder,
                         0, slitflats->subcols);
            free_cvector(myslit->framename, 0, CATREC_LEN);
            free_cvector(myslit->sigmaname, 0, CATREC_LEN);
            free_cvector(myslit->badname, 0, CATREC_LEN);
            free_cvector(myslit->boundname, 0, CATREC_LEN);
        }
    }
    /* free the old slit pointer */
    free(slitflats->slit);
    /* put the new pointer in slit */
    slitflats->slit = newslit;
    /* update the number of flats in the structure */
    slitflats->nflats = nframes;
    /* free temporary variables */
    free_ivector(framelist, 0, slitflats->nflats - 1);
    free_ivector(toclear, 0, slitflats->nflats - 1);

    /* to be even stricter, check whether the orders actually overlap;
   if not, I will simply put everything in one frame */
    /* of course, just do this if there is more than one frame left in the
   set of slit FF frames... */
    if (slitflats->nflats > 1) {
        /* run a loop over orders (from the second to the last) and x and find
     the absolute minimum of order separation */
        double fcurrmin = fabs((double) (slitflats->subrows + 1) * slitflats->substepy);
        for (iorder = 1; iorder <= ordpos->lastorder - ordpos->firstorder;
                        iorder++) {
            order = (double) (iorder + ordpos->firstorder);
            for (ix = 0; ix <= (slitflats->subcols - 1); ix++) {
                /* bail out if the function call return an error status */
                x = (double) (ix + slitflats->substartx);
                if ((status = get_ordpos(ordpos, order, x, &currcentre)) != NOERR) {
                    return (status);
                }
                double prevorder = (double) (iorder - 1 + ordpos->firstorder);
                if ((status = get_ordpos(ordpos, prevorder, x, &prevcentre)) != NOERR) {
                    return (status);
                }
                if (fabs(currcentre - prevcentre) < fcurrmin) {
                    fcurrmin = fabs(currcentre - prevcentre);
                }
            }
        }
        /* now I know the lowest order separation, is there overlap? */
        firstslit = slitflats->slit;
        slitFF* lastslit = firstslit + slitflats->nflats - 1;
        if (firstslit->yshift - firstslit->halfwidth + fcurrmin
                        - (lastslit->yshift + lastslit->halfwidth) > slitflats->substepy) {
            /* no overlap, therefore put all pixels in the first frame! */
            dataframe = fdmatrix(0, slitflats->subrows - 1, 0,
                            slitflats->subcols - 1);
            fdvecbuf4 = dataframe[0];
            memset(fdvecbuf4, 0,
                   slitflats->subrows * slitflats->subcols * sizeof(frame_data));
            sigmaframe = fdmatrix(0, slitflats->subrows - 1, 0,
                            slitflats->subcols - 1);
            fdvecbuf5 = sigmaframe[0];
            memset(fdvecbuf5, 0,
                   slitflats->subrows * slitflats->subcols * sizeof(frame_data));
            badframe = fmmatrix(0, slitflats->subrows - 1, 0, slitflats->subcols - 1);
            fmvecbuf3 = badframe[0];
            for (iyixindex = 0; iyixindex <= iyixuplimit; iyixindex++) {
                fmvecbuf3[iyixindex] = 1;
            }
            for (iorder = 0; iorder <= ordpos->lastorder - ordpos->firstorder;
                            iorder++) {
                iorderixoffset = iorder * slitflats->subcols;
                for (ix = 0; ix <= (slitflats->subcols - 1); ix++) {
                    iorderixindex = iorderixoffset + ix;
                    lvecbuf5 = lvecbuf3;
                    for (iframe = 0; iframe <= slitflats->nflats - 1; iframe++) {
                        myslit = slitflats->slit + iframe;
                        fdvecbuf6 = myslit->data[0];
                        fdvecbuf7 = myslit->sigma[0];
                        fmvecbuf4 = myslit->badpixel[0];
                        lvecbuf6 = myslit->highbound[0];
                        for (iy = lvecbuf5[iorderixindex]; iy <= lvecbuf6[iorderixindex];
                                        iy++) {
                            iyixindex = (iy * slitflats->subcols) + ix;
                            fdvecbuf4[iyixindex] = fdvecbuf6[iyixindex];
                            fdvecbuf5[iyixindex] = fdvecbuf7[iyixindex];
                            fmvecbuf3[iyixindex] = fmvecbuf4[iyixindex];
                        }
                        lvecbuf5 = lvecbuf6;
                    }
                    lvecbuf4[iorderixindex] = lvecbuf2[iorderixindex];
                }
            }
            /* now the ugly memory handling */
            /* copy the pointers to the new slit */
            newslit = (slitFF *) calloc(1, sizeof(slitFF));
            newslit->data = dataframe;
            newslit->sigma = sigmaframe;
            newslit->badpixel = badframe;
            newslit->framename = firstslit->framename;
            newslit->sigmaname = firstslit->sigmaname;
            newslit->badname = firstslit->badname;
            newslit->boundname = firstslit->boundname;
            newslit->yshift = (firstslit->yshift - firstslit->halfwidth
                            + lastslit->yshift + lastslit->halfwidth) / 2;
            newslit->halfwidth = (lastslit->yshift + lastslit->halfwidth
                            - firstslit->yshift + firstslit->halfwidth) / 2;
            newslit->lowbound = firstslit->lowbound;
            newslit->highbound = firstslit->highbound;
            /* free unneeded arrays */
            free_fdmatrix(firstslit->data, 0, slitflats->subrows, 0,
                          slitflats->subcols);
            free_fdmatrix(firstslit->sigma, 0, slitflats->subrows, 0,
                          slitflats->subcols);
            free_fmmatrix(firstslit->badpixel, 0, slitflats->subrows, 0,
                          slitflats->subcols);
            for (iframe = 1; iframe <= slitflats->nflats - 1; iframe++) {
                myslit = firstslit + iframe;
                free_fdmatrix(myslit->data, 0, slitflats->subrows, 0,
                              slitflats->subcols);
                free_fdmatrix(myslit->sigma, 0, slitflats->subrows, 0,
                              slitflats->subcols);
                free_fmmatrix(myslit->badpixel, 0, slitflats->subrows, 0,
                              slitflats->subcols);
                free_lmatrix(myslit->lowbound, 0,
                             ordpos->lastorder - ordpos->firstorder, 0, slitflats->subcols);
                free_lmatrix(myslit->highbound, 0,
                             ordpos->lastorder - ordpos->firstorder, 0, slitflats->subcols);
                free_cvector(myslit->framename, 0, CATREC_LEN);
                free_cvector(myslit->sigmaname, 0, CATREC_LEN);
                free_cvector(myslit->badname, 0, CATREC_LEN);
                free_cvector(myslit->boundname, 0, CATREC_LEN);
            }
            /* free the old slit pointer */
            free(slitflats->slit);
            /* replace it with the new pointer */
            slitflats->slit = newslit;
            /* set the number of flats in the structure to 1 */
            slitflats->nflats = 1;
        }
    }

    /* time to write to disk, isn't it? */

    return NOERR;

}

static int yshiftcompare(const void* s1, const void *s2) {
    const slitFF *slit1 = (const slitFF *) s1;
    const slitFF *slit2 = (const slitFF *) s2;

    if (slit1->yshift < slit2->yshift) {
        return (-1);
    } else if (slit1->yshift > slit2->yshift) {
        return (1);
    } else {
        return (0);
    }
}