GRAVI Pipeline Reference Manual 1.8.0
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gravi_vis.c
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1/* $Id: gravi_vis.c,v 1.10 2014/11/12 15:10:40 nazouaoui Exp $
2 *
3 * This file is part of the GRAVI Pipeline
4 * Copyright (C) 2002,2003 European Southern Observatory
5 *
6 * This program is free software; you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation; either version 2 of the License, or
9 * (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program; if not, write to the Free Software
18 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19 */
20
35/*
36 * History
37 * 21.11.2018 memory leak in gravi_average_self_visphi
38 * changes marked as 'EKW'
39 * 11/01/2019 Fix Warning parameter 'ret'
40 */
41/*-----------------------------------------------------------------------------
42 Includes
43 -----------------------------------------------------------------------------*/
44
45#ifdef HAVE_CONFIG_H
46#include <config.h>
47#endif
48
49#include <cpl.h>
50#include <string.h>
51#include <stdio.h>
52#include <math.h>
53#include <time.h>
54#include <complex.h>
55#include <string.h>
56#include <float.h>
57
58#include "gravi_data.h"
59#include "gravi_dfs.h"
60#include "gravi_pfits.h"
61#include "gravi_cpl.h"
62
63#include "gravi_utils.h"
64
65#include "gravi_vis.h"
66#include "gravi_eop.h"
67#include "gravi_tf.h"
68#include "gravi_idp.h"
69
70/*-----------------------------------------------------------------------------
71 Private prototypes
72 -----------------------------------------------------------------------------*/
73
74double gravi_randn (void);
75
76cpl_error_code gravi_array_online_variance(cpl_array * data, cpl_array * mean, cpl_array * variance, int n);
77cpl_error_code gravi_array_online_variance_res(cpl_array ** data,
78 int n, int rephase);
79cpl_error_code gravi_flux_average_bootstrap(cpl_table * oi_flux_avg,
80 cpl_table * oi_flux,
81 int nboot,
82 double outlier_threshold);
83cpl_error_code gravi_t3_average_bootstrap(cpl_table * oi_t3_avg,
84 cpl_table * oi_vis,
85 cpl_table * oi_flux,
86 int nboot,
87 int use_vFactor,
88 int use_pFactor,
89 double outlier_threshold);
90cpl_error_code gravi_vis_average_bootstrap (cpl_table * oi_vis_avg,
91 cpl_table * oi_vis2_avg,
92 cpl_table * oi_vis,
93 int nboot,
94 const char * phase_ref,
95 int use_vFactor,
96 int use_pFactor,
97 int use_debiasing,
98 double outlier_threshold);
99
100cpl_error_code gravi_vis_flag_nan (cpl_table * oi_table);
101
102cpl_error_code gravi_vis_average_amp (cpl_table *oi_table, const char *name, const char *err, int nbase);
103cpl_error_code gravi_vis_average_phi (cpl_table *oi_table, const char *name, const char *err, int nbase);
104cpl_error_code gravi_vis_average_value (cpl_table *oi_table, const char *name, const char *err, int nbase);
105cpl_error_code gravi_vis_resamp_amp (cpl_table * oi_table, const char * name, const char * err,
106 cpl_size nsamp, cpl_size nwave_new);
107cpl_error_code gravi_vis_resamp_phi (cpl_table * oi_table, const char * name, const char * err,
108 cpl_size nsamp, cpl_size nwave_new);
109cpl_error_code gravi_vis_smooth_amp (cpl_table * oi_table, const char * name, const char * err,
110 cpl_size nsamp);
111cpl_error_code gravi_vis_smooth_phi (cpl_table * oi_table, const char * name, const char * err,
112 cpl_size nsamp);
113
114cpl_error_code gravi_vis_fit_amp (cpl_table * oi_table, const char * name,
115 const char * err, cpl_size maxdeg);
116
117cpl_error_code gravi_vis_compute_column_mean (cpl_table * out_table,
118 cpl_table * in_table,
119 const char * name, int ntel);
120
121cpl_error_code gravi_vis_flag_median (cpl_table * oi_table, const char * data, const char *flag, double value);
122
123cpl_error_code gravi_average_self_visphi(cpl_table * oi_vis_avg,
124 cpl_table * oi_vis,
125 cpl_array * wavenumber,
126 const char * phase_ref, int* cmin, int* cmax, int nrange);
127
128double gdAbacusErrPhi(double x);
129
130/*-----------------------------------------------------------------------------
131 Function code
132 -----------------------------------------------------------------------------*/
133
134/*----------------------------------------------------------------------------*/
138/*----------------------------------------------------------------------------*/
139
140double gravi_randn (void)
141{
142 int nsamp = 50;
143 double samp[] = {0.97446388, 0.78404357, 2.24226141, 1.85507201, 1.10792943,
144 1.34028771, -0.15399594, 0.07316682, 1.60898976, 0.33111245,
145 0.76767625, -2.1252529 , 0.3898138 , 2.1218198 , 0.51703696,
146 0.38451722, 1.07581416, -0.61435275, 1.91926679, 1.10020069,
147 1.82407999, 1.07367663, 0.46105875, 0.45497282, 1.65549611,
148 1.21647974, -0.32725523, -0.36477508, 0.43947414, 1.0242778 ,
149 2.05617949, 1.06163165, 1.24564147, 2.36249995, 0.20676319,
150 1.30886256, 0.7122533 , 2.28503709, 0.7134141 , -0.19104819,
151 2.9925884 , 0.95761567, 2.11770457, 0.34763896, 0.30040327,
152 2.3535165 , 1.65839907, 1.89819461, 1.67480833, 1.11174145};
153
154 /* FIXME: build a better normal random generator !! */
155 return samp[rand()%nsamp];
156}
157
158
159/*-----------------------------------------------------------------------------*/
160
161cpl_error_code gravi_array_online_variance(cpl_array * data, cpl_array * mean, cpl_array * variance, int n)
162{
163 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
164 cpl_ensure_code (mean, CPL_ERROR_NULL_INPUT);
165 cpl_ensure_code (variance, CPL_ERROR_NULL_INPUT);
166 cpl_ensure_code (n>=0, CPL_ERROR_ILLEGAL_INPUT);
167
168 double delta = 0.0;
169 double rdata = 0.0;
170 double rmean = 0.0;
171 double n1 = 1. / ( (double)n + 1.0 );
172 double n2 = (double)n / ( (double)n + 1.0 );
173
174 cpl_size size = cpl_array_get_size (data);
175
176 /* delta = (x - mean)/(n+1)
177 mean = mean + delta
178 M2 = M2*n/(n+1) + delta*(x - mean) */
179
180 cpl_size w;
181 int nv = 0.0;
182 for (w = 0; w < size; w ++) {
183 /* delta = (x - mean)/(n+1) */
184 rdata = cpl_array_get (data, w, &nv);
185 rmean = cpl_array_get (mean, w, &nv);
186 delta = ( rdata - rmean ) * n1;
187 /* mean = mean + delta */
188 rmean = rmean + delta;
189 cpl_array_set (mean, w, rmean);
190 /* M2 = M2*n/(n+1) + delta*(x - mean) */
191 cpl_array_set (variance, w,
192 cpl_array_get (variance, w, &nv) * n2 + delta * ( rdata - rmean ));
193 }
194
195 int code;
196 if ( (code=cpl_error_get_code()) ) {
197 return cpl_error_set_message(cpl_func, code, "Cannot do online variance");
198 }
199
200 return CPL_ERROR_NONE;
201}
202
203/*-----------------------------------------------------------------------------*/
219/*-----------------------------------------------------------------------------*/
220
221cpl_error_code gravi_array_online_variance_res(cpl_array ** data,
222 int n, int rephase)
223{
225 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
226 cpl_ensure_code (n>=0, CPL_ERROR_ILLEGAL_INPUT);
227
228 cpl_size size = cpl_array_get_size (data[0]);
229 cpl_msg_debug(cpl_func,"Start function");
230
231 /* If first boot, we init the runnning mean and running variance
232 * and we store in the first array */
233 if ( n == 0 ) {
234 cpl_array_add (data[2], data[0]);
235 }
236
237 /* Recenter phase around the mean phase before computing its VARIANCE */
238 if (rephase) {
239 for (int w=0; w<size; w++ ) {
240 cpl_array_set (data[0], w,
241 carg( cexp (1*I* (cpl_array_get(data[0], w, NULL) -
242 cpl_array_get(data[2], w, NULL))) ) );
243 }
244 }
245
246 /* Run the gravi_online */
247 gravi_array_online_variance(data[0], data[1], data[3], n);
248
249 /* Free the current boot to prepare for next integration */
250 cpl_array_fill_window (data[0], 0, size, 0.0);
251
252 CPLCHECK_MSG ("Error in online variance");
253
255 return CPL_ERROR_NONE;
256}
257
258/*-----------------------------------------------------------------------------*/
272/*-----------------------------------------------------------------------------*/
273
274cpl_error_code gravi_flux_average_bootstrap(cpl_table * oi_flux_avg,
275 cpl_table * oi_flux,
276 int nboot,
277 double outlier_threshold)
278{
280 cpl_ensure_code (oi_flux_avg, CPL_ERROR_ILLEGAL_OUTPUT);
281 cpl_ensure_code (oi_flux, CPL_ERROR_NULL_INPUT);
282 cpl_ensure_code (nboot>0, CPL_ERROR_ILLEGAL_INPUT);
283
284 /* parameters */
285 int nv = 0, ntel = 4;
286 cpl_size nrow = cpl_table_get_nrow (oi_flux) / ntel;
287 cpl_size nwave = cpl_table_get_column_depth (oi_flux, "FLUX");
288
289 /* Pointer to columns, to speed-up */
290 cpl_array ** pFLUX = cpl_table_get_data_array (oi_flux, "FLUX");
291 cpl_array ** pFLUXERR = cpl_table_get_data_array (oi_flux, "FLUXERR");
292 cpl_array ** pFLAG = cpl_table_get_data_array (oi_flux, "FLAG");
293 double * pINTTIME = cpl_table_get_data_double (oi_flux, "INT_TIME");
294 double * pMJD = cpl_table_get_data_double (oi_flux, "MJD");
295 CPLCHECK_MSG ("Cannot get the data");
296
297 /* Loop on tel */
298 for (cpl_size tel = 0; tel < ntel; tel++) {
299
300 /* Tel for base and base for closure */
301 cpl_size nvalid = 0;
302
303 /* Arrays to store the final, integrated quantities
304 * 0: current boot, 1: running_mean, 2: first boot, 3: variance */
305 cpl_array **flux_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
306 double total_exptime = 0.0, mjd_avg = 0.0;
307
308 /*
309 * (0) Optimize the number of segment
310 */
311
312 /* Get the number of non-rejected frames */
313 int * flag = cpl_malloc( sizeof(int) * nrow );
314 for ( int row=0 ; row<nrow; row++ ) {
315 flag[row] = 0; nvalid++;
316 }
317
318 /* Build an optimal number of segment and nrow_per_segment */
319 cpl_size nrow_per_seg = CPL_MAX(nvalid / CPL_MIN (nrow, 100), 1);
320 cpl_size nseg = nvalid / nrow_per_seg;
321
322 /* Ensure there are at least 5 samples to bootstrap on,
323 * if no add montecarlo samples */
324 cpl_size nsamp = 5, nmontecarlo = CPL_MAX (nsamp - nseg, 0);
325
326 cpl_msg_info ("Stat", "%6lld valid frames over %6lld (%5.1f%%), make %4lld seg. of %5lld (miss %lld), add %lld MonteCarlo",
327 nvalid, nrow, (double)nvalid/(double)nrow*100.0,
328 nseg, nrow_per_seg, nvalid - nseg*nrow_per_seg, nmontecarlo);
329
330 /* Case we have at least one valid frame */
331 if ( nvalid > 0 ) {
332
333 /*
334 * (1) Pre-integration over segment, to bootstrap on less statistic
335 */
336
337 cpl_array **flux = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
338
339 /* Loop on segment */
340 cpl_size row = -1;
341 for ( int seg = 0 ; seg < nseg + nmontecarlo; seg ++ ) {
342 cpl_msg_debug(cpl_func,"pre integration of seg %d start with row %lld", seg, row);
343
344 /* Find nrow_per_seg valid frame to integrate in this segment */
345 cpl_size r = 0;
346 while ( r < nrow_per_seg ) {
347 row = (row + 1) % nrow;
348 if ( flag[row] ) {continue;} else {r++;}
349
350 /* Get indices */
351 cpl_size rtel = row * ntel + tel;
352
353 /* Compute the total integration time.
354 * Do not integrate for the MonteCarlo samples */
355 if (seg < nseg) {
356 total_exptime += pINTTIME[rtel];
357 mjd_avg += pMJD[rtel] * pINTTIME[rtel];
358 }
359
360 /* fast-no-CPL integration: get pointers on data */
361 double * tflux = cpl_array_get_data_double (flux[seg]);
362
363 /* Loop on wave */
364 for ( int w=0; w<nwave; w++ ) {
365 double FLUX = cpl_array_get (pFLUX[rtel], w, NULL);
366 double FLUXERR = cpl_array_get (pFLUXERR[rtel], w, NULL);
367 int outlier_flag = cpl_array_get (pFLAG[rtel], w, NULL);
368 CPLCHECK_MSG ("Cannot get data");
369
370 /* Reject outlier */
371 if (outlier_flag) {
372 FLUX = 0.0;
373 }
374 /* Add noise if this is a Monte Carlo sample. */
375 if ( seg > nseg-1 ) {
376 FLUX += 2 * FLUXERR * gravi_randn();
377 }
378
379 /* flux = < FLUX > over the frames in [e] */
380 tflux[w] += FLUX;
381
382 } /* End loop on wave */
383 } /* End loop on rows in this segment */
384 }/* End loop on segments */
385
386 /*
387 * (2) Compute the variance by bootstraping on the segments
388 */
389
390 /* Loop on bootstramp to compute the avg and the
391 * variance by the bootstraping methode */
392 srand(1);
393
394 for ( int boot = 0 ; boot < nboot ; boot ++ ) {
395 cpl_msg_debug(cpl_func,"Bootstrap %d over %d", boot+1, nboot);
396
397 /* Integrate nseg segment randomly selected.
398 * This loop is vectorialized in spectral direction */
399 for (int rowb = 0; rowb < nseg; rowb ++){
400
401 /* For the first bootstrap, we use all observed samples
402 * For the others, we also includes the possible montecarlo
403 * FIXME: verify the uniformity of rand for small nrows */
404 int rows;
405 if (boot == 0 ) rows = rowb;
406 else rows = rand()%(nseg+nmontecarlo);
407
408 /* Integrate the flux of selected segments */
409 cpl_array_add (flux_res[0], flux[rows]);
410 }
411 /* End loop on selected segments */
412
413 /* Compute the VARIANCE over the bootstraped samples with the 'online_variance' algorithm.
414 * See https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance */
415 gravi_array_online_variance_res (flux_res, boot, 0);
416
417 CPLCHECK_MSG("while computing the variances over the bootstrap");
418 }
419 /* End Loop on bootstrap */
420
421 /* Free list of segments and running mean */
422 FREELOOP (cpl_array_delete, flux, nseg + nmontecarlo);
423
424 /* Convert variance from bootstrap to RMS */
425 cpl_msg_debug(cpl_func,"Put the RMS over bootstrap");
426 cpl_array_power (flux_res[3], 0.5);
427 CPLCHECK_MSG("while converting variance -> rms");
428
429 /* Normalise integration */
430 mjd_avg /= total_exptime;
431
432 }
433
434 /*
435 * Step (1,2) in case there are no valid frames at all
436 */
437 if (nvalid == 0) {
438 cpl_msg_debug (cpl_func,"Not valid frames, force zero and infinit RMS");
439 cpl_array_fill_window (flux_res[3], 0, nwave, 1e10);
440 mjd_avg = cpl_table_get_column_mean (oi_flux, "MJD");
441 }
442
443 /* Renormalise by the number of outliers.
444 Also flag channels with too much outliers. */
445 cpl_array ** pflag = cpl_table_get_data_array (oi_flux_avg, "FLAG");
446 cpl_array * array = gravi_table_get_column_sum_array (oi_flux, "FLAG", tel, ntel);
447 CPLCHECK_MSG("cannot get data");
448
449 for (int wave = 0; wave < nwave; wave++) {
450 double value = cpl_array_get (array, wave, NULL) / nrow;
451 if (value < 1.0) {
452 cpl_array_set (flux_res[2], wave, cpl_array_get (flux_res[2], wave, NULL) / (1.0 - value));
453 }
454 if (value > outlier_threshold) {
455 cpl_array_set (pflag[tel], wave, 1);
456 }
457 }
458 FREE (cpl_array_delete, array);
459
460 /*
461 * (3) Save the results on the oi_flux_avg tables
462 */
463
464 cpl_table_set_array (oi_flux_avg, "FLUX", tel, flux_res[2]);
465 cpl_table_set_array (oi_flux_avg, "FLUXERR", tel, flux_res[3]);
466 CPLCHECK_MSG("filling FLUX and FLUXERR");
467
468 /* Flag the data with >100% error */
469 gravi_vis_flag_relative_threshold (oi_flux_avg, "FLUXERR", "FLUX", "FLAG", 1.0);
470 gravi_vis_flag_lower (oi_flux_avg, "FLUXERR", "FLAG", 0.0);
471 CPLCHECK_MSG("cannot flag baddata data");
472
473 /* Compute the total integration time */
474 cpl_msg_debug(cpl_func,"Total integration time = %.3f s", total_exptime);
475 cpl_table_set_double (oi_flux_avg, "INT_TIME", tel, total_exptime);
476 cpl_table_set_double (oi_flux_avg, "MJD", tel, mjd_avg);
477 cpl_table_set (oi_flux_avg, "NVALID", tel, nvalid);
478 cpl_table_set (oi_flux_avg, "NDIT", tel, nrow);
479
480 /* Set the TARGET_ID and STA_INDEX */
481 cpl_table_set_int (oi_flux_avg, "TARGET_ID", tel, cpl_table_get_int (oi_flux, "TARGET_ID", tel, &nv));
482 cpl_table_set_int (oi_flux_avg, "STA_INDEX", tel, cpl_table_get_int (oi_flux, "STA_INDEX", tel, &nv));
483
484 FREELOOP (cpl_array_delete, flux_res, 4);
485 cpl_free(flag);
486
487 } /* End loop on tel */
488
490 return CPL_ERROR_NONE;
491}
492
493/*-----------------------------------------------------------------------------*/
508/*-----------------------------------------------------------------------------*/
509
510cpl_error_code gravi_t3_average_bootstrap(cpl_table * oi_t3_avg,
511 cpl_table * oi_vis,
512 cpl_table * oi_flux,
513 int nboot,
514 int use_vFactor,
515 int use_pFactor,
516 double outlier_threshold)
517{
519 cpl_ensure_code (oi_t3_avg, CPL_ERROR_ILLEGAL_OUTPUT);
520 cpl_ensure_code (oi_vis, CPL_ERROR_NULL_INPUT);
521 cpl_ensure_code (oi_flux, CPL_ERROR_NULL_INPUT);
522 cpl_ensure_code (nboot>0, CPL_ERROR_ILLEGAL_INPUT);
523
524 /* Tel for base and base for closure
525 * Assume all the observations are made with the same array geometry.
526 * sta_index_t3[0] <-> tel1[clo[j][0]] = tel1[clo[j][2]]
527 * sta_index_t3[1] <-> tel1[clo[j][1]] = tel2[clo[j][0]]
528 * sta_index_t3[2] <-> tel2[clo[j][2]] = tel2[clo[j][1]]
529 */
530 int nv = 0, nbase = 6, ntel = 4, nclo = 4;
531
532 cpl_size nrow = cpl_table_get_nrow (oi_vis) / nbase;
533 cpl_size nwave = cpl_table_get_column_depth (oi_vis, "VISDATA");
534
535 /* Pointer to column, to speed-up */
536 cpl_array ** pVISDATA = cpl_table_get_data_array (oi_vis, "VISDATA");
537 cpl_array ** pVISERR = cpl_table_get_data_array (oi_vis, "VISERR");
538 cpl_array ** pFLUX = cpl_table_get_data_array (oi_flux, "FLUX");
539 cpl_array ** pFLAG = cpl_table_get_data_array (oi_vis, "FLAG");
540 double * pINTTIME = cpl_table_get_data_double (oi_vis, "INT_TIME");
541 double * pMJD = cpl_table_get_data_double (oi_vis, "MJD");
542 double * pUCOORD = cpl_table_get_data_double (oi_vis, "UCOORD");
543 double * pVCOORD = cpl_table_get_data_double (oi_vis, "VCOORD");
544 cpl_array ** pVFACTOR = use_vFactor?cpl_table_get_data_array (oi_vis, "V_FACTOR"):NULL;
545 /* awkwardness for scalar PFACTOR if SC, array over wave if FT */
546 double *pPFACTOR = NULL;
547 cpl_array **ppPFACTOR = NULL;
548 if (use_pFactor) {
549 if (cpl_table_get_column_depth(oi_vis, "P_FACTOR") > 0) {
550 ppPFACTOR = cpl_table_get_data_array(oi_vis, "P_FACTOR");
551 } else {
552 pPFACTOR = cpl_table_get_data_double(oi_vis, "P_FACTOR");
553 }
554 }
555
556 CPLCHECK_MSG ("Cannot get the data");
557
558 /* Loop on closure */
559 for (cpl_size closure = 0; closure < nclo; closure++) {
560
561 cpl_size nvalid = 0;
562 int base0 = GRAVI_CLO_BASE[closure][0];
563 int base1 = GRAVI_CLO_BASE[closure][1];
564 int base2 = GRAVI_CLO_BASE[closure][2];
565 int ctel0 = GRAVI_CLO_TEL[closure][0];
566 int ctel1 = GRAVI_CLO_TEL[closure][1];
567 int ctel2 = GRAVI_CLO_TEL[closure][2];
568
569 /* Arrays to store the final, integrated quantities
570 * 0: current boot, 1: running_mean, 2: first boot, 3: variance */
571 cpl_array **t3Amp_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
572 cpl_array **t3Phi_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
573 double total_exptime = 0.0, mjd_avg = 0.0;
574 double u1Coord = 0.0, v1Coord = 0.0, u2Coord = 0.0, v2Coord = 0.0;
575
576 /*
577 * (0) Optimize the number of segment
578 */
579
580 /* Get the number of non-rejected frames */
581 int * flag = cpl_table_get_data_int (oi_vis, "REJECTION_FLAG");
582 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_INPUT);
583 int * flagclo = cpl_malloc( sizeof(int) * nrow );
584 for ( int row=0 ; row<nrow; row++ ) {
585 flagclo[row] = flag[row * nbase + base0] + flag[row * nbase + base1] + flag[row * nbase + base2];
586 if ( flagclo[row] == 0 ) nvalid++;
587 }
588
589 /* Build an optimal number of segment and nrow_per_segment */
590 cpl_size nrow_per_seg = CPL_MAX (nvalid / CPL_MIN (nrow, 100), 1);
591 cpl_size nseg = nvalid / nrow_per_seg;
592
593 /* Ensure there are at least 5 samples to bootstrap on,
594 * if no add montecarlo samples */
595 cpl_size nsamp = 5, nmontecarlo = CPL_MAX (nsamp - nseg, 0);
596
597 cpl_msg_info ("Stat", "%6lld valid frames over %6lld (%5.1f%%), make %4lld seg. of %5lld (miss %lld), add %lld MonteCarlo",
598 nvalid, nrow, (double)nvalid/(double)nrow*100.0,
599 nseg, nrow_per_seg, nvalid - nseg*nrow_per_seg, nmontecarlo);
600
601 /* Case we have at least one valid frame */
602 if ( nvalid > 0 ) {
603
604 /*
605 * (1) Pre-integration over segment, to bootstrap on less statistic
606 */
607
608 cpl_array **bisp = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE_COMPLEX, nwave);
609 cpl_array **F012 = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
610
611 /* Loop on segment */
612 cpl_size row = -1;
613 for ( int seg = 0 ; seg < nseg + nmontecarlo ; seg ++ ) {
614 cpl_msg_debug(cpl_func,"pre integration of seg %d start with row %lld", seg, row);
615
616 /* Find nrow_per_seg valid frame to integrate in this segment */
617 cpl_size r = 0;
618 while ( r < nrow_per_seg ) {
619 row = (row + 1) % nrow;
620 if ( flagclo[row] ) {continue;} else {r++;}
621
622 /* Get indices */
623 cpl_size rbase0 = row * nbase + base0;
624 cpl_size rbase1 = row * nbase + base1;
625 cpl_size rbase2 = row * nbase + base2;
626
627 /* Compute the total integration time.
628 * Do not integrate for the MonteCarlo samples */
629 if (seg < nseg) {
630 total_exptime += pINTTIME[rbase0];
631 mjd_avg += pMJD[rbase0] * pINTTIME[rbase0];
632 u1Coord += pUCOORD[rbase0] * pINTTIME[rbase0];
633 v1Coord += pVCOORD[rbase0] * pINTTIME[rbase0];
634 u2Coord += pUCOORD[rbase1] * pINTTIME[rbase0];
635 v2Coord += pVCOORD[rbase1] * pINTTIME[rbase0];
636 }
637
638 /* fast-no-CPL integration: get pointers on data */
639 double complex * tbisp = cpl_array_get_data_double_complex (bisp[seg]);
640 double *tF012 = cpl_array_get_data_double (F012[seg]);
641 CPLCHECK_MSG ("Cannot get data");
642
643 double PFACTOR0 = 1.0, PFACTOR1 = 1.0, PFACTOR2 = 1.0;
644 if (use_pFactor && ppPFACTOR == NULL) { /* SC */
645 PFACTOR0 = pPFACTOR[rbase0];
646 PFACTOR1 = pPFACTOR[rbase1];
647 PFACTOR2 = pPFACTOR[rbase2];
648 if (use_pFactor == 2) {
649 PFACTOR0 *= PFACTOR0;
650 PFACTOR1 *= PFACTOR1;
651 PFACTOR2 *= PFACTOR2;
652 }
653 CPLCHECK_MSG ("Cannot get PFACTOR data");
654 }
655
656 /* Loop on wave */
657 for ( int w=0; w<nwave; w++ ) {
658 if (use_pFactor && ppPFACTOR) { /* FT */
659 pPFACTOR = cpl_array_get_data_double(ppPFACTOR[rbase0]);
660 PFACTOR0 = pPFACTOR[w];
661 pPFACTOR = cpl_array_get_data_double(ppPFACTOR[rbase1]);
662 PFACTOR1 = pPFACTOR[w];
663 pPFACTOR = cpl_array_get_data_double(ppPFACTOR[rbase2]);
664 PFACTOR2 = pPFACTOR[w];
665 if (use_pFactor == 2) {
666 PFACTOR0 *= PFACTOR0;
667 PFACTOR1 *= PFACTOR1;
668 PFACTOR2 *= PFACTOR2;
669 }
670 CPLCHECK_MSG ("Cannot get PFACTOR data");
671 }
672
673 double complex Vis0 = cpl_array_get_complex (pVISDATA[rbase0], w, NULL);
674 double complex Vis1 = cpl_array_get_complex (pVISDATA[rbase1], w, NULL);
675 double complex Vis2 = cpl_array_get_complex (pVISDATA[rbase2], w, NULL);
676 double complex VisErr0 = cpl_array_get_complex (pVISERR[rbase0], w, NULL);
677 double complex VisErr1 = cpl_array_get_complex (pVISERR[rbase1], w, NULL);
678 double complex VisErr2 = cpl_array_get_complex (pVISERR[rbase2], w, NULL);
679 double F0 = cpl_array_get (pFLUX[row * ntel + ctel0], w, NULL);
680 double F1 = cpl_array_get (pFLUX[row * ntel + ctel1], w, NULL);
681 double F2 = cpl_array_get (pFLUX[row * ntel + ctel2], w, NULL);
682 double VFACTOR0 = (use_vFactor?cpl_array_get (pVFACTOR[rbase0], w, NULL):1.0);
683 double VFACTOR1 = (use_vFactor?cpl_array_get (pVFACTOR[rbase1], w, NULL):1.0);
684 double VFACTOR2 = (use_vFactor?cpl_array_get (pVFACTOR[rbase2], w, NULL):1.0);
685 int outlier_flag0 = cpl_array_get (pFLAG[rbase0], w, NULL);
686 int outlier_flag1 = cpl_array_get (pFLAG[rbase1], w, NULL);
687 int outlier_flag2 = cpl_array_get (pFLAG[rbase2], w, NULL);
688
689 /* Reject outlier */
690 if (outlier_flag0 || outlier_flag1 || outlier_flag2) {
691 Vis0 = 0.0+0.0*I;
692 Vis1 = 0.0+0.0*I;
693 Vis2 = 0.0+0.0*I;
694 VisErr0 = 0.0+0.0*I;
695 VisErr1 = 0.0+0.0*I;
696 VisErr2 = 0.0+0.0*I;
697 F0 = 0.0;
698 F1 = 0.0;
699 F2 = 0.0;
700 }
701
702 /* Add noise if this is a Monte Carlo sample.
703 * APPROX: Noise is only added to the coherent fluxes */
704 if ( seg > nseg-1 ) {
705 Vis0 += 1.*I * cimag(VisErr0) * gravi_randn();
706 Vis0 += 1. * creal(VisErr0) * gravi_randn();
707 Vis1 += 1.*I * cimag(VisErr1) * gravi_randn();
708 Vis1 += 1. * creal(VisErr1) * gravi_randn();
709 Vis2 += 1.*I * cimag(VisErr2) * gravi_randn();
710 Vis2 += 1. * creal(VisErr2) * gravi_randn();
711 }
712
713 /* bisp = < v1*v2*conj(v3) > over the frames in [e^3] */
714 tbisp[w] += Vis0 * Vis1 * conj (Vis2);
715
716 /* F012 = < F0*F1*F2 > over the frames in [e^3]
717 * corrected from expected visibility losses */
718 tF012[w] += F0 * F1 * F2 *
719 sqrt (CPL_MAX (VFACTOR0 * VFACTOR1 * VFACTOR2 *
720 PFACTOR0 * PFACTOR1 * PFACTOR2, 0.0));
721
722 } /* End loop on wave */
723 } /* End loop on rows in this segment */
724 }/* End loop on segments */
725
726 /*
727 * (2) Compute the variance by bootstraping on the segments
728 */
729
730 /* Loop on bootstramp to compute the avg and the
731 * variance by the bootstraping methode */
732 srand(1);
733
734 for ( int boot = 0 ; boot < nboot ; boot ++ ) {
735 cpl_msg_debug(cpl_func,"Bootstrap %d over %d", boot+1, nboot);
736
737 /* Init the integration of nseg segment randomly selected */
738 cpl_array * bisp_boot = gravi_array_init_double_complex (nwave, 0.0 + I*0.0);
739 cpl_array * f012_boot = gravi_array_init_double (nwave, 0.0);
740
741 /* Integrate nseg segment randomly selected.
742 * This loop is vectorialized in spectral direction */
743 for (int rowb = 0; rowb < nseg; rowb ++){
744
745 /* For the first bootstrap, we use all observed samples
746 * For the others, we also includes the possible montecarlo
747 * FIXME: verify the uniformity of rand for small nrows */
748 int rows;
749 if (boot == 0 ) rows = rowb;
750 else rows = rand()%(nseg+nmontecarlo);
751
752 /* Integrate the bispectre and flux of selected segments */
753 cpl_array_add (bisp_boot, bisp[rows]);
754 cpl_array_add (f012_boot, F012[rows]);
755 }
756 /* End loop on selected segments */
757
758 /* Make sure the geometric flux is not null */
759 gravi_array_threshold_min (f012_boot, 1e-15);
760
761 /* Compute the argument and the module of the bispectrum */
762 FREE (cpl_array_delete, t3Amp_res[0]);
763 t3Amp_res[0] = cpl_array_duplicate(bisp_boot);
764 cpl_array_abs (t3Amp_res[0]);
765 cpl_array_divide (t3Amp_res[0], f012_boot);
766
767 FREE (cpl_array_delete, t3Phi_res[0]);
768 t3Phi_res[0] = cpl_array_duplicate(bisp_boot);
769 cpl_array_arg (t3Phi_res[0]);
770
771 /* Compute the VARIANCE over the bootstraped samples with the 'online_variance' algorithm.
772 * See https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance */
773 gravi_array_online_variance_res (t3Amp_res, boot, 0);
774 gravi_array_online_variance_res (t3Phi_res, boot, 1);
775
776 FREE (cpl_array_delete, bisp_boot);
777 FREE (cpl_array_delete, f012_boot);
778 CPLCHECK_MSG("while computing the variances over the bootstrap");
779 }
780 /* End Loop on bootstrap */
781
782 /* Free list of segments and running mean */
783 FREELOOP (cpl_array_delete, bisp, nseg + nmontecarlo);
784 FREELOOP (cpl_array_delete, F012, nseg + nmontecarlo);
785
786 /* Convert variance from bootstrap to RMS */
787 cpl_msg_debug(cpl_func,"Put the RMS over bootstrap");
788 cpl_array_power (t3Phi_res[3], 0.5);
789 cpl_array_power (t3Amp_res[3], 0.5);
790 CPLCHECK_MSG("while converting variance -> rms");
791
792 /* Normalizase integration */
793 mjd_avg /= total_exptime;
794 u1Coord /= total_exptime;
795 v1Coord /= total_exptime;
796 u2Coord /= total_exptime;
797 v2Coord /= total_exptime;
798
799 }
800
801 /*
802 * Step (1,2) in case there are no valid frames at all
803 */
804 if (nvalid == 0) {
805 cpl_msg_debug (cpl_func,"Not valid frames, force zero and infinit RMS");
806 cpl_array_fill_window (t3Amp_res[3], 0, nwave, 1e10);
807 cpl_array_fill_window (t3Phi_res[3], 0, nwave, 1e10);
808 mjd_avg = cpl_table_get_column_mean (oi_vis, "MJD");
809 }
810
811 /* Flag channels with too much outliers. */
812 cpl_array ** pflag = cpl_table_get_data_array (oi_t3_avg, "FLAG");
813 CPLCHECK_MSG("cannot get data");
814
815 cpl_array * array = cpl_array_new (nwave, CPL_TYPE_INT);
816 cpl_array_fill_window (array, 0, nwave, 0.0);
817 int * sum_flag = cpl_array_get_data_int (array);
818
819 for (int row=0; row < nrow; row++) {
820 cpl_array * arr0 = pFLAG[row * nbase + base0];
821 cpl_array * arr1 = pFLAG[row * nbase + base1];
822 cpl_array * arr2 = pFLAG[row * nbase + base2];
823 for (int wave = 0; wave < nwave; wave++) {
824 if (cpl_array_get (arr0, wave, NULL) ||
825 cpl_array_get (arr1, wave, NULL) ||
826 cpl_array_get (arr2, wave, NULL) )
827 sum_flag[wave] ++;
828 }
829 }
830
831 for (int wave = 0; wave < nwave; wave++) {
832 double value = cpl_array_get (array, wave, NULL) / nrow;
833 if (value > outlier_threshold) {
834 cpl_array_set (pflag[closure], wave, 1);
835 }
836 }
837 FREE (cpl_array_delete, array);
838
839 /*
840 * (3) Save the results on the oi_t3_avg tables
841 */
842
843 /* Save the cloture amplitude on the oi_T3 tables */
844 cpl_table_set_array (oi_t3_avg, "T3AMP", closure, t3Amp_res[2]);
845 cpl_table_set_array (oi_t3_avg, "T3AMPERR", closure, t3Amp_res[3]);
846 CPLCHECK_MSG("filling T3AMP");
847
848 /* Save the cloture phase on the oi_T3 tables */
849 gravi_table_set_array_phase (oi_t3_avg, "T3PHI", closure, t3Phi_res[2]);
850 gravi_table_set_array_phase (oi_t3_avg, "T3PHIERR", closure, t3Phi_res[3]);
851 CPLCHECK_MSG("filling T3PHI");
852
853 /* Flag the data with >100% error or >60deg error or negative errors */
854 gravi_vis_flag_threshold (oi_t3_avg, "T3PHIERR", "FLAG", 60.0);
855 gravi_vis_flag_threshold (oi_t3_avg, "T3AMPERR", "FLAG", 1.0);
856 gravi_vis_flag_lower (oi_t3_avg, "T3AMPERR", "FLAG", 0.0);
857 gravi_vis_flag_median (oi_t3_avg, "T3PHIERR", "FLAG", 5.0);
858 CPLCHECK_MSG("cannot flag baddata data");
859
860 /* Compute the total integration time and MJD */
861 cpl_msg_debug(cpl_func,"Total integration time = %.3f s", total_exptime);
862 cpl_table_set_double (oi_t3_avg, "INT_TIME", closure, total_exptime);
863 cpl_table_set_double (oi_t3_avg, "MJD", closure, mjd_avg);
864 cpl_table_set_double (oi_t3_avg, "U1COORD", closure, u1Coord);
865 cpl_table_set_double (oi_t3_avg, "V1COORD", closure, v1Coord);
866 cpl_table_set_double (oi_t3_avg, "U2COORD", closure, u2Coord);
867 cpl_table_set_double (oi_t3_avg, "V2COORD", closure, v2Coord);
868 cpl_table_set (oi_t3_avg, "NVALID", closure, nvalid);
869 cpl_table_set (oi_t3_avg, "NDIT", closure, nrow);
870
871 /* Set the TARGET_ID */
872 cpl_table_set_int (oi_t3_avg, "TARGET_ID", closure, cpl_table_get_int (oi_vis, "TARGET_ID", base0, &nv));
873
874 /* Set STA_INDEX */
875 cpl_array * sta_index = cpl_array_new (3, CPL_TYPE_INT);
876 cpl_array_set_int (sta_index, 0, cpl_table_get_int (oi_flux,"STA_INDEX", ctel0, &nv));
877 cpl_array_set_int (sta_index, 1, cpl_table_get_int (oi_flux,"STA_INDEX", ctel1, &nv));
878 cpl_array_set_int (sta_index, 2, cpl_table_get_int (oi_flux,"STA_INDEX", ctel2, &nv));
879 cpl_table_set_array (oi_t3_avg, "STA_INDEX", closure, sta_index);
880 FREE (cpl_array_delete, sta_index);
881
882 /* Free the aggregate flags for closures */
883 FREELOOP (cpl_array_delete, t3Phi_res, 4);
884 FREELOOP (cpl_array_delete, t3Amp_res, 4);
885 FREE (cpl_free, flagclo);
886
887 } /* End loop on closure */
888
890 return CPL_ERROR_NONE;
891}
892
893/*-----------------------------------------------------------------------------*/
913/*-----------------------------------------------------------------------------*/
914
915cpl_error_code gravi_vis_average_bootstrap (cpl_table * oi_vis_avg,
916 cpl_table * oi_vis2_avg,
917 cpl_table * oi_vis,
918 int nboot,
919 const char * phase_ref,
920 int use_vFactor,
921 int use_pFactor,
922 int use_debiasing,
923 double outlier_threshold)
924{
926 cpl_ensure_code (oi_vis_avg, CPL_ERROR_ILLEGAL_OUTPUT);
927 cpl_ensure_code (oi_vis2_avg, CPL_ERROR_ILLEGAL_OUTPUT);
928 cpl_ensure_code (oi_vis, CPL_ERROR_NULL_INPUT);
929 cpl_ensure_code (nboot>0, CPL_ERROR_ILLEGAL_INPUT);
930
931 /* Parameters */
932 int nv = 0, nbase = 6;
933 cpl_size nrow = cpl_table_get_nrow (oi_vis) / nbase;
934 cpl_size nwave = cpl_table_get_column_depth (oi_vis, "VISDATA");
935
936 /* Pointer to columns, to speed-up */
937 cpl_array ** pVISDATA = cpl_table_get_data_array (oi_vis, "VISDATA");
938 cpl_array ** pVISERR = cpl_table_get_data_array (oi_vis, "VISERR");
939 cpl_array ** pFNORM = cpl_table_get_data_array (oi_vis, "F1F2");
940 cpl_array ** pFLAG = cpl_table_get_data_array (oi_vis, "FLAG");
941 double * pINTTIME = cpl_table_get_data_double (oi_vis, "INT_TIME");
942 double * pMJD = cpl_table_get_data_double (oi_vis, "MJD");
943 double * pUCOORD = cpl_table_get_data_double (oi_vis, "UCOORD");
944 double * pVCOORD = cpl_table_get_data_double (oi_vis, "VCOORD");
945 cpl_array ** pVFACTOR = use_vFactor?cpl_table_get_data_array (oi_vis, "V_FACTOR"):NULL;
946 /* awkwardness for scalar PFACTOR if SC, array over wave if FT */
947 double *pPFACTOR = NULL;
948 cpl_array **ppPFACTOR = NULL;
949 if (use_pFactor) {
950 if (cpl_table_get_column_depth(oi_vis, "P_FACTOR") > 0) {
951 ppPFACTOR = cpl_table_get_data_array(oi_vis, "P_FACTOR");
952 } else {
953 pPFACTOR = cpl_table_get_data_double(oi_vis, "P_FACTOR");
954 }
955 }
956 CPLCHECK_MSG ("Cannot get the data");
957
958 /* Get the reference phase */
959 cpl_array ** pPHASEREF = NULL;
960 if (phase_ref && strcmp (phase_ref, "NONE"))
961 pPHASEREF = cpl_table_get_data_array (oi_vis, phase_ref);
962 CPLCHECK_MSG ("Cannot get the reference phase data (column missing?)");
963
964 /* Loop on base */
965 for (cpl_size base = 0; base < nbase; base ++) {
966
967 /* Tel for base */
968 cpl_size nvalid = 0;
969
970 /* Arrays to store the final, integrated quantities
971 * 0: current boot, 1: running_mean, 2: first boot, 3: variance */
972 cpl_array **visR_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
973 cpl_array **visI_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
974 cpl_array **vis2_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
975 cpl_array **visAmp_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
976 cpl_array **visPhi_res = gravi_array_new_list (4, CPL_TYPE_DOUBLE, nwave);
977 double total_exptime = 0.0, mjd_avg = 0.0;
978 double uCoord = 0.0, vCoord = 0.0;
979
980 /*
981 * (0) Optimize the number of segment
982 */
983
984 /* Get the number of non-rejected frames */
985 int * flag = cpl_table_get_data_int (oi_vis, "REJECTION_FLAG");
986 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_INPUT);
987 for ( int row=0 ; row<nrow; row++ ) if ( flag[row * nbase + base] == 0 ) nvalid++;
988
989 /* Build an optimal number of segment and nrow_per_segment */
990 cpl_size nrow_per_seg = CPL_MAX (nvalid / CPL_MIN (nrow, 100), 1);
991 cpl_size nseg = nvalid / nrow_per_seg;
992
993 /* Ensure there are at least 5 samples to bootstrap on,
994 * if no add montecarlo samples */
995 cpl_size nsamp = 5, nmontecarlo = CPL_MAX (nsamp - nseg, 0);
996
997 cpl_msg_info ("Stat", "%6lld valid frames over %6lld (%5.1f%%), make %4lld seg. of %5lld (miss %lld), add %lld MonteCarlo",
998 nvalid, nrow, (double)nvalid/(double)nrow*100.0,
999 nseg, nrow_per_seg, nvalid - nseg*nrow_per_seg, nmontecarlo);
1000
1001 /* Case we have at least one valid frame */
1002 if ( nvalid > 0 ) {
1003
1004 /*
1005 * (1) Pre-integration over segment, to bootstrap on less statistic
1006 */
1007 cpl_array **visR = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
1008 cpl_array **visI = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
1009 cpl_array **POWER = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
1010 cpl_array **F12 = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
1011 cpl_array **F1F2 = gravi_array_new_list (nseg + nmontecarlo, CPL_TYPE_DOUBLE, nwave);
1012
1013 /* Loop on segment */
1014 cpl_size row = -1;
1015 for ( int seg = 0 ; seg < nseg + nmontecarlo ; seg ++ ) {
1016 cpl_msg_debug(cpl_func,"pre integration of seg %d start with row %lld", seg, row);
1017
1018 /* Find nrow_per_seg valid frame to integrate in this segment */
1019 cpl_size r = 0;
1020 while ( r < nrow_per_seg ) {
1021 row = (row + 1) % nrow;
1022 if ( flag[row * nbase + base] ) {continue;} else {r++;}
1023
1024 /* Get indices */
1025 cpl_size rbase = row * nbase + base;
1026
1027 /* Compute the total integration time.
1028 * Do not integrate for the MonteCarlo samples */
1029 if (seg < nseg) {
1030 total_exptime += pINTTIME[rbase];
1031 mjd_avg += pMJD[rbase] * pINTTIME[rbase];
1032 uCoord += pUCOORD[rbase] * pINTTIME[rbase];
1033 vCoord += pVCOORD[rbase] * pINTTIME[rbase];
1034 }
1035
1036 /* fast-no-CPL integration: get pointers on data */
1037 double *tR = cpl_array_get_data_double (visR[seg]);
1038 double *tI = cpl_array_get_data_double (visI[seg]);
1039 double *tP = cpl_array_get_data_double (POWER[seg]);
1040 double *tF1F2 = cpl_array_get_data_double (F1F2[seg]);
1041 double *tF12 = cpl_array_get_data_double (F12[seg]);
1042 CPLCHECK_MSG ("Cannot get data");
1043
1044 double PFACTOR = 1.0;
1045 if (use_pFactor && ppPFACTOR == NULL) { /* SC */
1046 PFACTOR = pPFACTOR[rbase];
1047 if (use_pFactor == 2) PFACTOR *= PFACTOR;
1048 CPLCHECK_MSG ("Cannot get PFACTOR data");
1049 }
1050
1051 /* Loop on wave */
1052 for (int w = 0; w < nwave; w++) {
1053 if (use_pFactor && ppPFACTOR) { /* FT */
1054 pPFACTOR = cpl_array_get_data_double(ppPFACTOR[rbase]);
1055 PFACTOR = pPFACTOR[w];
1056 if (use_pFactor == 2) PFACTOR *= PFACTOR;
1057 CPLCHECK_MSG ("Cannot get PFACTOR data");
1058 }
1059 double VFACTOR = use_vFactor?cpl_array_get (pVFACTOR[rbase], w, NULL):1.0;
1060 double PHASEREF = pPHASEREF?cpl_array_get (pPHASEREF[rbase], w, NULL):0.0;
1061 double FNORM = cpl_array_get (pFNORM[rbase], w, NULL);
1062 double complex Vis = cpl_array_get_complex (pVISDATA[rbase], w, NULL);
1063 double complex VErr = cpl_array_get_complex (pVISERR[rbase], w, NULL);
1064 double mR = creal (Vis);
1065 double mI = cimag (Vis);
1066 double eR = creal (VErr);
1067 double eI = cimag (VErr);
1068 int outlier_flag = cpl_array_get (pFLAG[rbase], w, NULL);
1069 CPLCHECK_MSG ("Cannot get data");
1070
1071 /* Reject outlier */
1072 if (outlier_flag) {
1073 mR = 0.0; mI = 0.0;
1074 eR = 0.0; eI = 0.0;
1075 FNORM = 0.0;
1076 }
1077
1078 /* Add noise if this is a Monte Carlo sample.
1079 * APPROX: Noise is only added to the coherent flux */
1080 if ( seg > nseg-1 ) {
1081 mR += 2 * eR * gravi_randn();
1082 mI += 2 * eI * gravi_randn();
1083 }
1084 if (PHASEREF) {
1085 /* Integrate <R> and <I> rephased */
1086 tR[w] += cos(PHASEREF) * mR - sin(PHASEREF) * mI;
1087 tI[w] += cos(PHASEREF) * mI + sin(PHASEREF) * mR;
1088 } else {
1089 /* Integrate directly without rephasing */
1090 tR[w] += mR;
1091 tI[w] += mI;
1092 }
1093
1094 /* Compute the flux <F1F2> and <sqrt(|F1F2|)> x sign(F1F2)
1095 * corrected by the vFactor if needed */
1096 tF1F2[w] += FNORM * VFACTOR * PFACTOR;
1097 tF12[w] += sqrt( CPL_MAX (FNORM * VFACTOR * PFACTOR, 0.0) );
1098
1099 /* Integrate < R2 + I2 - sR2 - sI2 > */
1100 if (use_debiasing) {
1101 tP[w] += mR*mR + mI*mI - eR*eR - eI*eI;
1102 } else {
1103 tP[w] += mR*mR + mI*mI;
1104 }
1105 } /* End loop on wave */
1106 } /* End loop on rows in this segment */
1107 } /* End loop on segments */
1108
1109
1110 /*
1111 * (2) Compute the variance by bootstraping on the segments
1112 */
1113
1114 /* Loop on bootstramp to compute the avg and the
1115 * variance by the bootstraping methode */
1116 srand(1);
1117
1118 for ( int boot = 0 ; boot < nboot ; boot ++ ) {
1119 cpl_msg_debug (cpl_func,"Bootstrap %d over %d", boot+1, nboot);
1120
1121 /* Init the itegration of nseg segments */
1122 cpl_array * F12_boot = gravi_array_init_double (nwave, 0.0);
1123 cpl_array * F1F2_boot = gravi_array_init_double (nwave, 0.0);
1124
1125 /* Integrate nseg segments randomly selected.
1126 * This loop is vectorialized in spectral direction */
1127 for (int rowb = 0; rowb < nseg; rowb ++) {
1128
1129 /* For the first bootstrap, we use all observed samples
1130 * For the others, we also includes the possible montecarlo
1131 * FIXME: verify the uniformity of rand for small nrows */
1132 int rows;
1133 if (boot == 0 ) rows = rowb;
1134 else rows = rand()%(nseg+nmontecarlo);
1135
1136 /* Integrate the selected segments */
1137 cpl_array_add (visR_res[0], visR[rows]);
1138 cpl_array_add (visI_res[0], visI[rows]);
1139 cpl_array_add (vis2_res[0], POWER[rows]);
1140 cpl_array_add (F12_boot, F12[rows]);
1141 cpl_array_add (F1F2_boot, F1F2[rows]);
1142 }
1143 /* End loop to integrate nseg segments randomly selected
1144 * We now have a random realisation of a high SNR dataset
1145 * to which we can apply the estimators */
1146
1147 /* Make sure the geometric flux is not null */
1148 gravi_array_threshold_min (F1F2_boot, 1e-15);
1149
1150 /* Energy estimator
1151 vis2 = POWER / F1F2 */
1152 cpl_array_divide (vis2_res[0], F1F2_boot);
1153 CPLCHECK_MSG("while computing the energie integration");
1154
1155 /* Norm of coherent integration
1156 visAmp = sqrt(visR^2 + visR^2) / F12 */
1157 FREE (cpl_array_delete, visAmp_res[0]);
1158 visAmp_res[0] = gravi_array_compute_norm2 (visR_res[0], visI_res[0]);
1159 cpl_array_power (visAmp_res[0], 0.5);
1160 cpl_array_divide (visAmp_res[0], F12_boot);
1161 CPLCHECK_MSG("while computing the norm of the coherent integration");
1162
1163 /* Phase of coherent integration
1164 visPhi = arctan( visI, visR ) */
1165 FREE (cpl_array_delete, visPhi_res[0]);
1166 visPhi_res[0] = gravi_array_wrap_complex (visR_res[0], visI_res[0]);
1167 cpl_array_arg (visPhi_res[0]);
1168
1169 /* Compute the VARIANCE over the bootstraped samples with the 'online_variance' algorithm.
1170 * See https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance */
1171 gravi_array_online_variance_res (vis2_res, boot, 0);
1172 gravi_array_online_variance_res (visAmp_res, boot, 0);
1173 gravi_array_online_variance_res (visR_res, boot, 0);
1174 gravi_array_online_variance_res (visI_res, boot, 0);
1175 gravi_array_online_variance_res (visPhi_res, boot, 1);
1176 CPLCHECK_MSG("while computing the variances over the bootstrap");
1177
1178 /* Delete these temporary integrations */
1179 FREE (cpl_array_delete, F12_boot);
1180 FREE (cpl_array_delete, F1F2_boot);
1181 CPLCHECK_MSG("while freeing during bootstrap");
1182 }
1183 /* End bootstrap */
1184
1185 /* Free list of segments */
1186 FREELOOP (cpl_array_delete, visR, nseg + nmontecarlo);
1187 FREELOOP (cpl_array_delete, visI, nseg + nmontecarlo);
1188 FREELOOP (cpl_array_delete, POWER, nseg + nmontecarlo);
1189 FREELOOP (cpl_array_delete, F12, nseg + nmontecarlo);
1190 FREELOOP (cpl_array_delete, F1F2, nseg + nmontecarlo);
1191
1192 /* Convert variance from bootstrap to RMS */
1193 cpl_msg_debug (cpl_func,"Put the RMS over bootstrap");
1194 cpl_array_power (vis2_res[3], 0.5);
1195 cpl_array_power (visAmp_res[3], 0.5);
1196 cpl_array_power (visPhi_res[3], 0.5);
1197 cpl_array_power (visR_res[3], 0.5);
1198 cpl_array_power (visI_res[3], 0.5);
1199 CPLCHECK_MSG ("while converting variance -> rms");
1200
1201 /* Normalize integration */
1202 mjd_avg /= total_exptime;
1203 uCoord /= total_exptime;
1204 vCoord /= total_exptime;
1205 }
1206
1207 /*
1208 * Step (1,2) in case there are no valid frames at all
1209 */
1210 if (nvalid == 0) {
1211 cpl_msg_debug (cpl_func,"Not valid frames, force zero and infinit RMS");
1212 cpl_array_fill_window (vis2_res[3], 0, nwave, 1e10);
1213 cpl_array_fill_window (visR_res[3], 0, nwave, 1e10);
1214 cpl_array_fill_window (visI_res[3], 0, nwave, 1e10);
1215 cpl_array_fill_window (visAmp_res[3], 0, nwave, 1e10);
1216 cpl_array_fill_window (visPhi_res[3], 0, nwave, 1e10);
1217 mjd_avg = cpl_table_get_column_mean (oi_vis, "MJD");
1218 }
1219
1220 /* Renormalise by the number of outliers.
1221 Also flag channels with too much outliers. */
1222 cpl_array ** pflag_vis = cpl_table_get_data_array (oi_vis_avg, "FLAG");
1223 cpl_array ** pflag_vis2 = cpl_table_get_data_array (oi_vis2_avg, "FLAG");
1224 cpl_array * array = gravi_table_get_column_sum_array (oi_vis, "FLAG", base, nbase);
1225 CPLCHECK_MSG("cannot get data");
1226
1227 for (int wave = 0; wave < nwave; wave++) {
1228 double value = cpl_array_get (array, wave, NULL) / nrow;
1229 if (value < 1.0) {
1230 cpl_array_set (visR_res[2], wave, cpl_array_get (visR_res[2], wave, NULL) / (1.0 - value));
1231 cpl_array_set (visI_res[2], wave, cpl_array_get (visI_res[2], wave, NULL) / (1.0 - value));
1232 }
1233 if (value > outlier_threshold) {
1234 cpl_array_set (pflag_vis[base], wave, 1);
1235 cpl_array_set (pflag_vis2[base], wave, 1);
1236 }
1237 }
1238 FREE (cpl_array_delete, array);
1239
1240 /*
1241 * (3) Save the results on the oi_vis_avg tables
1242 */
1243
1244 cpl_table_set_array (oi_vis2_avg, "VIS2DATA", base, vis2_res[2]);
1245 cpl_table_set_array (oi_vis2_avg, "VIS2ERR", base, vis2_res[3]);
1246 CPLCHECK_MSG("filling VIS2");
1247
1248 gravi_table_set_array_double_complex (oi_vis_avg, "VISDATA", base, visR_res[2], visI_res[2]);
1249 gravi_table_set_array_double_complex (oi_vis_avg, "VISERR", base, visR_res[3], visI_res[3]);
1250 CPLCHECK_MSG("filling VISDATA");
1251
1252 cpl_table_set_array (oi_vis_avg, "RVIS", base, visR_res[2]);
1253 cpl_table_set_array (oi_vis_avg, "RVISERR", base, visR_res[3]);
1254 CPLCHECK_MSG("filling RVIS");
1255
1256 cpl_table_set_array (oi_vis_avg, "IVIS", base, visI_res[2]);
1257 cpl_table_set_array (oi_vis_avg, "IVISERR", base, visI_res[3]);
1258 CPLCHECK_MSG("filling IVIS");
1259
1260 cpl_table_set_array (oi_vis_avg, "VISAMP", base, visAmp_res[2]);
1261 cpl_table_set_array (oi_vis_avg, "VISAMPERR", base, visAmp_res[3]);
1262 CPLCHECK_MSG("filling VISAMP");
1263
1264 gravi_table_set_array_phase (oi_vis_avg, "VISPHI", base, visPhi_res[2]);
1265 gravi_table_set_array_phase (oi_vis_avg, "VISPHIERR", base, visPhi_res[3]);
1266 CPLCHECK_MSG("filling VISPHI");
1267
1268 /* Flag the data with >100% error or >60deg error */
1269 gravi_vis_flag_threshold (oi_vis2_avg, "VIS2ERR", "FLAG", 1.0);
1270 gravi_vis_flag_lower (oi_vis2_avg, "VIS2ERR", "FLAG", 0.0);
1271 gravi_vis_flag_median (oi_vis2_avg, "VIS2ERR", "FLAG", 5.0);
1272 gravi_vis_flag_threshold (oi_vis_avg, "VISAMPERR", "FLAG", 1.0);
1273 gravi_vis_flag_lower (oi_vis_avg, "VISAMPERR", "FLAG", 0.0);
1274 gravi_vis_flag_median (oi_vis_avg, "VISPHIERR", "FLAG", 5.0);
1275 CPLCHECK_MSG("cannot flag baddata data");
1276
1277 /* Compute the total integration time */
1278 cpl_table_set (oi_vis_avg, "INT_TIME", base, total_exptime);
1279 cpl_table_set (oi_vis2_avg, "INT_TIME", base, total_exptime);
1280 cpl_table_set (oi_vis_avg, "MJD", base, mjd_avg);
1281 cpl_table_set (oi_vis2_avg, "MJD", base, mjd_avg);
1282 cpl_table_set (oi_vis_avg, "UCOORD", base, uCoord);
1283 cpl_table_set (oi_vis_avg, "VCOORD", base, vCoord);
1284 cpl_table_set (oi_vis2_avg, "UCOORD", base, uCoord);
1285 cpl_table_set (oi_vis2_avg, "VCOORD", base, vCoord);
1286 CPLCHECK_MSG("cannot fill time");
1287
1288 /* Set some statistics */
1289 cpl_table_set (oi_vis2_avg, "NVALID", base, nvalid);
1290 cpl_table_set (oi_vis2_avg, "NDIT", base, nrow);
1291 cpl_table_set (oi_vis_avg, "NVALID", base, nvalid);
1292 cpl_table_set (oi_vis_avg, "NDIT", base, nrow);
1293 CPLCHECK_MSG("cannot fill nvalid");
1294
1295 /* Set the TARGET_ID and STA_INDEX */
1296 cpl_table_set_int (oi_vis_avg, "TARGET_ID", base, cpl_table_get_int (oi_vis, "TARGET_ID", base, &nv));
1297 cpl_table_set_int (oi_vis2_avg, "TARGET_ID", base, cpl_table_get_int (oi_vis, "TARGET_ID", base, &nv));
1298 cpl_table_set_array (oi_vis_avg, "STA_INDEX", base, cpl_table_get_array (oi_vis, "STA_INDEX", base));
1299 cpl_table_set_array (oi_vis2_avg, "STA_INDEX", base, cpl_table_get_array (oi_vis, "STA_INDEX", base));
1300
1301 /* Free variance */
1302 FREELOOP (cpl_array_delete, vis2_res, 4);
1303 FREELOOP (cpl_array_delete, visAmp_res, 4);
1304 FREELOOP (cpl_array_delete, visPhi_res, 4);
1305 FREELOOP (cpl_array_delete, visR_res, 4);
1306 FREELOOP (cpl_array_delete, visI_res, 4);
1307
1308 }
1309 /* End loop on bases */
1310
1312 return CPL_ERROR_NONE;
1313}
1314
1315double gdAbacusErrPhi(double x)
1340{
1341 const double Asymptot = CPL_MATH_PI / sqrt(3.0);
1342 double c[8] = {2.7191808010909,
1343 -17.1901043936273,
1344 45.0654103760899,
1345 -63.4441678243197,
1346 52.3098941426378,
1347 -25.8090699917488,
1348 7.84352873962491,
1349 -1.57308595820081};
1350
1351 double x2, x3, x4, x5, x6, x7, z;
1352 if (x > Asymptot) {
1353 return (1E10);
1354 }
1355 if (x > 1.74413) {
1356 return (0.691 / (Asymptot - x));
1357 }
1358 if (x < 0.1) {
1359 return (x);
1360 }
1361 x2 = x*x;
1362 x3 = x2*x;
1363 x4 = x2*x2;
1364 x5 = x3*x2;
1365 x6 = x3*x3;
1366 x7 = x6*x;
1367 z = c[0] * x7 + c[1] * x6 + c[2] * x5 + c[3] * x4 + c[4] * x3 + c[5] * x2 + c[6] * x + c[7];
1368 return pow(10, z);
1369}
1370
1371/*-----------------------------------------------------------------------------*/
1382/*-----------------------------------------------------------------------------*/
1383
1384cpl_error_code gravi_average_self_visphi(cpl_table * oi_vis_avg,
1385 cpl_table * oi_vis,
1386 cpl_array * wavenumber,
1387 const char * phase_ref, int* cmin, int* cmax, int nrange)
1388{
1390 cpl_ensure_code(oi_vis_avg, CPL_ERROR_ILLEGAL_OUTPUT);
1391 cpl_ensure_code(oi_vis, CPL_ERROR_NULL_INPUT);
1392
1393 /* Parameters */
1394 int nbase = 6;
1395 cpl_size nrow = cpl_table_get_nrow(oi_vis) / nbase;
1396 cpl_size nwave = cpl_table_get_column_depth(oi_vis, "VISDATA");
1397
1398 int use_crange = (nrange > 0);
1399 if (use_crange) {
1400 for (int i = 0; i < nrange; ++i) {
1401 if (cmax[i] - cmin[i] < 1) {
1402 use_crange = 0;
1403 break;
1404 }
1405 if (cmax[i] > nwave - 1) {
1406 use_crange = 0;
1407 break;
1408 }
1409 if (cmin[i] < 0) {
1410 use_crange = 0;
1411 break;
1412 }
1413 }
1414 if (use_crange) {
1415 for (int i = 0; i < nrange; ++i) cpl_msg_info("Reference Channel", "Part %02d [%3d:%3d]", i + 1, cmin[i], cmax[i]);
1416 } else {
1417 cpl_msg_info("Warning (SELF_VISPHI)", "Invalid Ranges Found, continuing with default Method.");
1418 }
1419 }
1420
1421 /* Pointer to columns, to speed-up */
1422 cpl_array ** pVISDATA = cpl_table_get_data_array(oi_vis, "VISDATA");
1423 cpl_array ** pVISERR = cpl_table_get_data_array(oi_vis, "VISERR");
1424 CPLCHECK_MSG("Cannot get the data");
1425
1426 /* Get the reference phase unless it has already been removed*/
1427 cpl_array ** pPHASEREF = NULL;
1428 if (phase_ref && strcmp(phase_ref, "NONE"))
1429 pPHASEREF = cpl_table_get_data_array(oi_vis, phase_ref);
1430 CPLCHECK_MSG("Cannot get the reference phase data (column missing?)");
1431
1432 /* Loop on base */
1433 for (cpl_size base = 0; base < nbase; base++) {
1434
1435 /* number of valid rows for base */
1436 cpl_size nvalid = 0;
1437
1438 /* Arrays to store the final, integrated quantities
1439 * 0: running_mean, 2: variance */
1440 cpl_array **visPhi_res = gravi_array_new_list(2, CPL_TYPE_DOUBLE, nwave);
1441
1442 /* Get the number of non-rejected frames */
1443 int * flag = cpl_table_get_data_int(oi_vis, "REJECTION_FLAG");
1444 cpl_ensure_code(flag, CPL_ERROR_ILLEGAL_INPUT);
1445 for (int row = 0; row < nrow; row++) if (flag[row * nbase + base] == 0) nvalid++;
1446
1447 cpl_msg_info("Stat (SELF_VISPHI)", "%6lld valid frames over %6lld (%5.1f%%)",
1448 nvalid, nrow, (double) nvalid / (double) nrow * 100.0);
1449
1450 /*
1451 * return in case there are no valid frames at all
1452 */
1453 if (nvalid == 0) {
1454 cpl_msg_debug(cpl_func, "No valid frames, force zero and infinite RMS");
1455 cpl_array_fill_window(visPhi_res[1], 0, nwave, 1e10);
1456 gravi_table_set_array_phase(oi_vis_avg, "VISPHI", base, visPhi_res[0]);
1457 gravi_table_set_array_phase(oi_vis_avg, "VISPHIERR", base, visPhi_res[1]);
1458 CPLCHECK_MSG("filling VISPHI");
1459 /* Free variance */
1460 FREELOOP(cpl_array_delete, visPhi_res, 2);
1461 break;
1462 }
1463
1464 cpl_array **Vis = gravi_array_new_list(nvalid, CPL_TYPE_DOUBLE_COMPLEX, nwave);
1465 cpl_array **EVis = gravi_array_new_list(nvalid, CPL_TYPE_DOUBLE_COMPLEX, nwave);
1466
1467 cpl_array **W1 = gravi_array_new_list(nvalid, CPL_TYPE_DOUBLE_COMPLEX, nwave);
1468 cpl_array **EW1 = gravi_array_new_list(nvalid, CPL_TYPE_DOUBLE_COMPLEX, nwave);
1469 /* Loop on row */
1470
1471 for (cpl_size currentRow = 0, validRowIndex = -1; currentRow < nrow; currentRow++) {
1472 if (flag[currentRow * nbase + base]) {
1473 continue;
1474 } else {
1475 /* Get indices */
1476 cpl_size rbase = currentRow * nbase + base;
1477 validRowIndex++;
1478
1479 /* fast-no-CPL integration: get pointers on data */
1480 double complex *ptrC = cpl_array_get_data_double_complex(Vis[validRowIndex]);
1481 double complex *ptrEC = cpl_array_get_data_double_complex(EVis[validRowIndex]);
1482 CPLCHECK_MSG("Cannot get data");
1483
1484 /* Loop on wave */
1485 for (int w = 0; w < nwave; w++) {
1486 double PHASEREF = pPHASEREF ? cpl_array_get(pPHASEREF[rbase], w, NULL) : 0.0;
1487 double complex vis = cpl_array_get_double_complex(pVISDATA[rbase], w, NULL);
1488 double complex viserr = cpl_array_get_double_complex(pVISERR[rbase], w, NULL);
1489 CPLCHECK_MSG("Cannot get data");
1490 if (PHASEREF) {
1491 /* rephase <R> and <I> */
1492 ptrC[w] = (cos(PHASEREF) * creal(vis) - sin(PHASEREF) * cimag(vis)) +
1493 I * (cos(PHASEREF) * cimag(vis) + sin(PHASEREF) * creal(vis));
1494 } else {
1495 /* no rephasing */
1496 ptrC[w] = vis;
1497 }
1498 ptrEC[w] = viserr;
1499 } /* End loop on wave */
1500 } /* End frame not flagged */
1501 } /* End loop on rows */
1502
1503 for (int irow = 0; irow < nvalid; irow++) {
1504
1505 /* Normalize the phasor to avoid bad pixels */
1506 /*
1507 cpl_array * norm = cpl_array_duplicate(Vis[irow]);
1508 cpl_array_abs(norm);
1509 cpl_array_divide(Vis[irow], norm);
1510 */
1511
1512 /* Compute and remove the mean group delay in [m] */
1513 double mean_delay = 0.0;
1514 gravi_array_get_group_delay_loop(&Vis[irow], NULL, wavenumber, &mean_delay, 1, 2e-3, CPL_FALSE);
1515 gravi_array_multiply_phasor(Vis[irow], -2 * I * CPL_MATH_PI * mean_delay, wavenumber);
1516
1517 /* Compute and remove the mean phase in [rad] */
1518 double mean_phase = carg(cpl_array_get_mean_complex(Vis[irow]));
1519 cpl_array_multiply_scalar_complex(Vis[irow], cexp(-I * mean_phase));
1520 }
1521
1522 cpl_array *CRef = cpl_array_new(nwave, CPL_TYPE_DOUBLE_COMPLEX);
1523 cpl_array *ECRef = cpl_array_new(nwave, CPL_TYPE_DOUBLE_COMPLEX);
1524 double complex *pCRef = cpl_array_get_data_double_complex(CRef);
1525 double complex *pECRef = cpl_array_get_data_double_complex(ECRef);
1526
1527 /* Production of the reference channel: mean of all R and I parts
1528 * of all channels except the one considered ( eq 2.3) */
1529 for (int irow = 0; irow < nvalid; irow++) {
1530 /*reset sum to 0 */
1531 double complex totalVis = 0.0 + I * 0.0;
1532 double complex totalEVis = 0.0 + I * 0.0;
1533 /* fast-no-CPL integration: get pointers on data */
1534 double complex *pVis = cpl_array_get_data_double_complex(Vis[irow]);
1535 double complex *pEVis = cpl_array_get_data_double_complex(EVis[irow]);
1536
1537 double complex *pW1 = cpl_array_get_data_double_complex(W1[irow]);
1538 double complex *pEW1 = cpl_array_get_data_double_complex(EW1[irow]);
1539
1540 CPLCHECK_MSG("Cannot get data");
1541 if (use_crange) {
1542 /* sum all Vis for this row */
1543 int nchans = 0;
1544 for (int i = 0; i < nrange; ++i) {
1545 for (int w = cmin[i]; w < cmax[i]; ++w) {
1546 totalVis += pVis[w];
1547 totalEVis += pEVis[w];
1548 nchans++;
1549 }
1550 }
1551 for (int w = 0; w < nwave; w++) {
1552 cpl_array_set_double_complex(CRef, w, totalVis / nchans);
1553 cpl_array_set_double_complex(ECRef, w, totalEVis / nchans);
1554 }
1555 } else {
1556 /* sum all Vis for this row */
1557 for (int w = 0; w < nwave; w++) {
1558 totalVis += pVis[w];
1559 totalEVis += pEVis[w];
1560 }
1561 /* then construct Cref by substracting current R and I
1562 * at that Wlen and make the arithmetic mean. The code permits
1563 * to avoid not only the channel itself removed but the 2*radius
1564 * around (not activated). */
1565 int iw = 0;
1566 int radius = 0;
1567 int divider = nwave - (2 * radius) - 1;
1568 for (; iw < radius; iw++) {
1569 cpl_array_set_double_complex(CRef, iw, totalVis / nwave);
1570 cpl_array_set_double_complex(ECRef, iw, totalEVis / nwave);
1571 }
1572 for (; iw < nwave - radius; iw++) {
1573 double complex tmp = 0.0 + I * 0.0;
1574 double complex Etmp = 0.0 + I * 0.0;
1575 for (int j = iw; j < iw + 2 * radius + 1; ++j) tmp += pVis[iw];
1576 cpl_array_set_double_complex(CRef, iw, (totalVis - tmp) / divider);
1577 for (int j = iw; j < iw + 2 * radius + 1; ++j) Etmp += pEVis[iw];
1578 cpl_array_set_double_complex(ECRef, iw, (totalEVis - Etmp) / divider);
1579 }
1580 for (; iw < radius; iw++) {
1581 cpl_array_set_double_complex(CRef, iw, totalVis / nwave);
1582 cpl_array_set_double_complex(ECRef, iw, totalEVis / nwave);
1583 }
1584 }
1585 /* Now the interspectrum is C*~C_Ref. Store in w1. */
1586 for (int w = 0; w < nwave; w++) {
1587 pW1[w] = pVis[w] * conj(pCRef[w]);
1588
1589 /* Please have a look to the F. Millour thesis
1590 (http://tel.archives-ouvertes.fr/tel-00134268),
1591 pp.91-92 (eq. 4.55 to 4.58) */
1592 pEW1[w] = (creal(pEVis[w]) * gravi_pow2(creal(pCRef[w])) +
1593 creal(pECRef[w]) * gravi_pow2(creal(pVis[w])) +
1594 cimag(pVis[w]) * gravi_pow2(cimag(pCRef[w])) +
1595 cimag(pECRef[w]) + gravi_pow2(cimag(pVis[w]))) +
1596
1597 I * (
1598 cimag(pVis[w]) * gravi_pow2(creal(pCRef[w])) +
1599 cimag(pECRef[w]) * gravi_pow2(creal(pVis[w])) +
1600 creal(pVis[w]) * gravi_pow2(cimag(pCRef[w])) +
1601 creal(pECRef[w]) + gravi_pow2(cimag(pVis[w]))
1602 );
1603 }
1604 }
1605
1606 FREE(cpl_array_delete, CRef);
1607 FREE(cpl_array_delete, ECRef);
1608 FREELOOP(cpl_array_delete, Vis, nvalid);
1609 FREELOOP(cpl_array_delete, EVis, nvalid);
1610
1611 double *pPhi = cpl_array_get_data_double(visPhi_res[0]);
1612 double *pPhiErr = cpl_array_get_data_double(visPhi_res[1]);
1613
1614 /* Compute mean VisPhi as average of selected frames. */
1615 for (int w = 0; w < nwave; w++) {
1616 cpl_array *cpxVisVect = cpl_array_new(nvalid, CPL_TYPE_DOUBLE_COMPLEX);
1617
1618 /* The W1 vector */
1619 for (int irow = 0; irow < nvalid; irow++) {
1620 const double complex *pW1 = cpl_array_get_data_double_complex_const(W1[irow]);
1621 cpl_array_set_double_complex(cpxVisVect, irow, pW1[w]);
1622 }
1623 /* The Phase Herself */
1624 /* average re and im */
1625 double complex w1Avg;
1626 w1Avg = cpl_array_get_mean_complex(cpxVisVect);
1627
1628 /* store */
1629 pPhi[w] = atan2(cimag(w1Avg), creal(w1Avg));
1630 /* WE USE THE STATISTICAL ERROR FOR BINNING */
1631 w1Avg = conj(w1Avg);
1632 cpl_array *Vect = cpl_array_new(nvalid, CPL_TYPE_DOUBLE);
1633 for (int irow = 0; irow < nvalid; irow++) {
1634 const double complex *tW1 = cpl_array_get_data_double_complex_const(W1[irow]);
1635 /* add w1*conj(w1Avg) to vector*/
1636 cpl_array_set_double(Vect, irow, atan2(cimag(tW1[w] * w1Avg), creal(tW1[w] * w1Avg)));
1637 }
1638 double x = cpl_array_get_stdev(Vect);
1639 /* Err on Phi must be corrected with an abacus*/
1640 pPhiErr[w] = gdAbacusErrPhi(x / sqrt(nvalid));
1641 /* START EKW 21/11/2018 */
1642 FREE(cpl_array_delete, cpxVisVect);
1643 FREE(cpl_array_delete, Vect);
1644 /* END EKW 21/11/2018 */
1645 }
1646
1647 gravi_table_set_array_phase(oi_vis_avg, "VISPHI", base, visPhi_res[0]);
1648 gravi_table_set_array_phase(oi_vis_avg, "VISPHIERR", base, visPhi_res[1]);
1649 CPLCHECK_MSG("filling VISPHI");
1650 /* Free variance */
1651 FREELOOP(cpl_array_delete, visPhi_res, 2);
1652 /* START EKW 21/11/2018 */
1653 FREELOOP(cpl_array_delete, EW1 , nvalid);
1654 FREELOOP(cpl_array_delete, W1 , nvalid);
1655 /* END EKW 21/11/2018 */
1656
1657 }
1658
1659 /* End loop on bases */
1660
1662 return CPL_ERROR_NONE;
1663}
1664
1665/*----------------------------------------------------------------------------*/
1674/*----------------------------------------------------------------------------*/
1675
1677 const cpl_parameterlist * parlist,
1678 cpl_size * current_frame)
1679{
1681 cpl_ensure (p2vmred_data, CPL_ERROR_NULL_INPUT, NULL);
1682 cpl_ensure (parlist, CPL_ERROR_NULL_INPUT, NULL);
1683
1684 int nv, nbase = 6, ntel = 4;
1685
1686 /*
1687 * Compute the limit of integration
1688 */
1689
1690 /* Get the current position and the maximum nb to integrate */
1691 cpl_size max_frame = gravi_param_get_int (parlist, "gravity.vis.max-frame");
1692 cpl_msg_info (cpl_func,"Average %lli frames starting from %lli",
1693 max_frame, *current_frame);
1694
1695
1696
1697 /* Get the SC DIT */
1698 cpl_propertylist * p2vmred_header = gravi_data_get_header (p2vmred_data);
1699 double dit_sc = gravi_pfits_get_dit_sc (p2vmred_header) * 1e6;
1700
1701 /* Get the vis_SC table for first polarisation */
1702 int npol_sc = gravi_pfits_get_pola_num (p2vmred_header, GRAVI_SC);
1703 cpl_table * vis_SC = gravi_data_get_oi_vis (p2vmred_data, GRAVI_SC, 0, npol_sc);
1704 cpl_size nrow = cpl_table_get_nrow (vis_SC) / nbase;
1705
1706 /* Get first and last frame for this integration */
1707 cpl_size sframe = *current_frame;
1708 cpl_size eframe = CPL_MIN (*current_frame + max_frame - 1, nrow-1);
1709
1710 /* Check if we reached the end of the file, or increment */
1711 if (eframe >= nrow-1) *current_frame = -1;
1712 else *current_frame += max_frame;
1713
1714 /* Compute start and end-time */
1715 double start_time, end_time;
1716 start_time = cpl_table_get (vis_SC, "TIME", sframe*nbase, &nv) - dit_sc/2;
1717 end_time = cpl_table_get (vis_SC, "TIME", eframe*nbase, &nv) + dit_sc/2;
1718
1719 /* Compute verbose */
1720 cpl_msg_info (cpl_func,"Integrate frames: first = %lli last = %lli", sframe, eframe);
1721 cpl_msg_info (cpl_func,"start = %f end = %f [s]", start_time*1e-6, end_time*1e-6);
1722
1723
1724 /*
1725 * Prepare the output
1726 */
1727
1728 cpl_msg_info(cpl_func, "Construction of the averaged output data");
1729
1730 gravi_data * vis_data = gravi_data_new (0);
1731 cpl_propertylist * vis_header = gravi_data_get_header (vis_data);
1732 cpl_propertylist_append (vis_header, p2vmred_header);
1733
1734 /* Copy the oi tables needed in output data.
1735 * This will duplicate all OI_WAVELENGTH tables */
1736 gravi_data_copy_ext (vis_data, p2vmred_data, GRAVI_OI_ARRAY_EXT);
1737 gravi_data_copy_ext (vis_data, p2vmred_data, GRAVI_OI_TARGET_EXT);
1738 gravi_data_copy_ext (vis_data, p2vmred_data, GRAVI_OI_WAVELENGTH_EXT);
1739
1740 CPLCHECK_NUL ("Cannot get tables for output data");
1741
1742 /*
1743 * Start with FT
1744 */
1745
1746 if (gravi_data_has_type (p2vmred_data, "_FT") <= 0 ) {
1747 cpl_msg_info (cpl_func, "P2VMRED data has no FT extensions");
1748 }
1749 else {
1750 /* Reduction parameters */
1751 int v_factor_flag_ft = 0;
1752 int p_factor_flag_ft = 0;
1753 const char *p_factor_str_ft = gravi_param_get_string (parlist, "gravity.vis.vis-correction-ft");
1754 if (!strcmp("PFACTOR", p_factor_str_ft))
1755 p_factor_flag_ft = 1;
1756 else if (!strcmp("PFACTOR_SQUARED", p_factor_str_ft))
1757 p_factor_flag_ft = 2;
1758 int debiasing_flag_ft = gravi_param_get_bool (parlist, "gravity.vis.debias-ft");
1759 int nboot_ft = gravi_param_get_int (parlist, "gravity.vis.nboot");
1760 const char * phase_ref_ft = "SELF_REF";
1761 double outlier_threshold_ft = 0.0;
1762 cpl_msg_info (cpl_func, "vFactor correction for FT is %s",v_factor_flag_ft?"ENABLE":"DISABLE");
1763 cpl_msg_info (cpl_func, "pFactor correction for FT is %s",(p_factor_flag_ft>0)?p_factor_str_ft:"DISABLE");
1764
1765 CPLCHECK_NUL("Cannot get parameters");
1766
1767 cpl_msg_info (cpl_func, "Bias subtraction of V2 for FT is %s",debiasing_flag_ft?"ENABLE":"DISABLE");
1768 cpl_msg_info (cpl_func, "Reference phase for FT is %s",phase_ref_ft);
1769
1770
1771 /*
1772 * Loop on polarisations
1773 */
1774 int npol_ft = gravi_pfits_get_pola_num (p2vmred_header, GRAVI_FT);
1775 for (int pol = 0; pol < npol_ft; pol++) {
1776 cpl_msg_info (cpl_func, "Start FT polarisation %d over %d",pol+1, npol_ft);
1777
1778 /* Get the input table of FT */
1779 cpl_table * vis_FT = gravi_data_get_oi_vis (p2vmred_data, GRAVI_FT, pol, npol_ft);
1780 cpl_table * flux_FT = gravi_data_get_oi_flux (p2vmred_data, GRAVI_FT, pol, npol_ft);
1781 int nwave_ft = cpl_table_get_column_depth (vis_FT, "VISDATA");
1782 CPLCHECK_NUL ("Cannot get data");
1783
1784 /* Create averated product */
1785 cpl_table * oi_vis2_FT = gravi_table_oi_create (nwave_ft, 1, GRAVI_OI_VIS2_EXT);
1786 gravi_table_new_column (oi_vis2_FT, "NDIT", NULL, CPL_TYPE_INT);
1787 gravi_table_new_column (oi_vis2_FT, "NVALID", NULL, CPL_TYPE_INT);
1788
1789 cpl_table * oi_vis_FT = gravi_table_oi_create (nwave_ft, 1, GRAVI_OI_VIS_EXT);
1790 gravi_table_new_column (oi_vis_FT, "NDIT", NULL, CPL_TYPE_INT);
1791 gravi_table_new_column (oi_vis_FT, "NVALID", NULL, CPL_TYPE_INT);
1792
1793 cpl_table * oi_T3_FT = gravi_table_oi_create (nwave_ft, 1, GRAVI_OI_T3_EXT);
1794 gravi_table_new_column (oi_T3_FT, "NDIT", NULL, CPL_TYPE_INT);
1795 gravi_table_new_column (oi_T3_FT, "NVALID", NULL, CPL_TYPE_INT);
1796
1797 cpl_table * oi_flux_FT = gravi_table_oi_create (nwave_ft, 1, GRAVI_OI_FLUX_EXT);
1798 gravi_table_new_column (oi_flux_FT, "NDIT", NULL, CPL_TYPE_INT);
1799 gravi_table_new_column (oi_flux_FT, "NVALID", NULL, CPL_TYPE_INT);
1800 CPLCHECK_NUL ("Cannot create product");
1801
1802 /* Keep only selected rows */
1803 vis_FT = gravi_table_extract_time_interval (vis_FT, start_time, end_time);
1804 flux_FT = gravi_table_extract_time_interval (flux_FT, start_time, end_time);
1805
1806 /*
1807 * Compute OIVIS2 and OIVIS for FT
1808 */
1809 cpl_msg_info (cpl_func, "Compute OIVIS2 and OIVIS for FT");
1810
1811 gravi_vis_average_bootstrap (oi_vis_FT, oi_vis2_FT, vis_FT,
1812 nboot_ft,
1813 phase_ref_ft,
1814 v_factor_flag_ft,
1815 p_factor_flag_ft,
1816 debiasing_flag_ft,
1817 outlier_threshold_ft);
1818 CPLCHECK_NUL("Cannot average the FT frames");
1819
1820 /*
1821 * Compute OIT3 for FT
1822 */
1823 cpl_msg_info (cpl_func, "Compute OIT3 for FT");
1824
1825 gravi_t3_average_bootstrap (oi_T3_FT, vis_FT, flux_FT,
1826 nboot_ft,
1827 v_factor_flag_ft,
1828 p_factor_flag_ft,
1829 outlier_threshold_ft);
1830 CPLCHECK_NUL("Cannot average t3 of FT");
1831
1832 /*
1833 * Compute OI_FLUX for FT
1834 */
1835 cpl_msg_info (cpl_func, "Compute OI_FLUX for FT");
1836
1837 gravi_flux_average_bootstrap (oi_flux_FT, flux_FT,
1838 nboot_ft,
1839 outlier_threshold_ft);
1840 CPLCHECK_NUL("Cannot average flux of FT");
1841
1842 /*
1843 * Add tables in the vis_data
1844 */
1845 cpl_propertylist * vis_plist = gravi_data_get_oi_vis_plist (p2vmred_data, GRAVI_FT, pol, npol_ft);
1846 cpl_propertylist * oivis_plist = cpl_propertylist_new();
1847 cpl_propertylist_copy_property (oivis_plist, vis_plist, "DATE-OBS");
1848 cpl_propertylist_copy_property (oivis_plist, vis_plist, "EXTVER");
1849 cpl_propertylist_copy_property (oivis_plist, vis_plist, "ARRNAME");
1850 cpl_propertylist_copy_property (oivis_plist, vis_plist, "INSNAME");
1851 cpl_propertylist_update_string (oivis_plist, "AMPTYP","absolute");
1852 cpl_propertylist_update_string (oivis_plist, "PHITYP","differential");
1853 cpl_propertylist_update_int (oivis_plist, "PHIORDER",1);
1854 gravi_data_add_table (vis_data, oivis_plist, GRAVI_OI_VIS_EXT, oi_vis_FT);
1855
1856 cpl_propertylist * oivis2_plist = cpl_propertylist_new();
1857 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "DATE-OBS");
1858 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "EXTVER");
1859 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "ARRNAME");
1860 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "INSNAME");
1861 gravi_data_add_table (vis_data, oivis2_plist, GRAVI_OI_VIS2_EXT, oi_vis2_FT);
1862
1863 cpl_propertylist * oit3_plist = cpl_propertylist_new();
1864 cpl_propertylist_copy_property (oit3_plist, vis_plist, "DATE-OBS");
1865 cpl_propertylist_copy_property (oit3_plist, vis_plist, "EXTVER");
1866 cpl_propertylist_copy_property (oit3_plist, vis_plist, "ARRNAME");
1867 cpl_propertylist_copy_property (oit3_plist, vis_plist, "INSNAME");
1868 gravi_data_add_table (vis_data, oit3_plist, GRAVI_OI_T3_EXT, oi_T3_FT);
1869
1870 cpl_propertylist * oiflux_plist = cpl_propertylist_new();
1871 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "DATE-OBS");
1872 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "EXTVER");
1873 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "ARRNAME");
1874 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "INSNAME");
1875 cpl_propertylist_update_string (oiflux_plist, "CALSTAT", "U");
1876 cpl_propertylist_set_comment (oiflux_plist, "CALSTAT", "Uncalibrated flux per telescope");
1877 gravi_data_add_table (vis_data, oiflux_plist, GRAVI_OI_FLUX_EXT, oi_flux_FT);
1878
1879 CPLCHECK_NUL ("Cannot add tables");
1880
1881 FREE (cpl_table_delete, vis_FT);
1882 FREE (cpl_table_delete, flux_FT);
1883
1884 } /* end loop on pol */
1885 } /* End FT */
1886
1887 /*
1888 * Then with SC
1889 */
1890
1891 if (gravi_data_has_type (p2vmred_data, "_SC") <= 0 ) {
1892 cpl_msg_info (cpl_func, "P2VMRED data has no SC extensions");
1893 }
1894 else {
1895
1896 /* Read the object separation. Actually should
1897 * be the mode maybe more than the separation */
1898 double SOBJ_X = gravi_pfits_get_sobj_x (p2vmred_header);
1899 double SOBJ_Y = gravi_pfits_get_sobj_y (p2vmred_header);
1900 double SOBJ_R = sqrt(SOBJ_X*SOBJ_X + SOBJ_Y*SOBJ_Y);
1901
1902 /* Reference phase requested by user, deal with AUTO */
1903 const char * phase_ref_sc = gravi_param_get_string (parlist, "gravity.vis.phase-ref-sc");
1904
1905 if ( !strcmp (phase_ref_sc,"AUTO") && SOBJ_R > 0.001)
1906 {
1907 phase_ref_sc = "IMAGING_REF";
1908 if (cpl_table_has_column (vis_SC, phase_ref_sc) == 0) {
1909 phase_ref_sc = "PHASE_REF";
1910 cpl_msg_warning (cpl_func, "No table 'IMAGING_REF', changing mode to phase_ref_sc='PHASE_REF'");
1911 CPLCHECK_NUL("tototo....");
1912 }
1913 }
1914 else if ( !strcmp (phase_ref_sc,"AUTO") && SOBJ_R < 0.001)
1915 phase_ref_sc = "PHASE_REF";
1916
1917 cpl_msg_info (cpl_func, "Reference phase for SC is %s",phase_ref_sc);
1918
1919 /* Output phase requested by user, deal with AUTO */
1920 const char * output_phase_sc = gravi_param_get_string (parlist, "gravity.vis.output-phase-sc");
1921
1922 if ( !strcmp (output_phase_sc,"AUTO") && SOBJ_R > 0.001)
1923 output_phase_sc = "ABSOLUTE";
1924 else if ( !strcmp (output_phase_sc,"AUTO") && SOBJ_R < 0.001)
1925 output_phase_sc = "DIFFERENTIAL";
1926
1927 /*
1928 force SELF_REF if SELF_VISPHI unless NONE has been selected (for what purpose?)
1929 */
1930 if (!strcmp(output_phase_sc, "SELF_VISPHI")) {
1931 if (strcmp(phase_ref_sc, "NONE")) {
1932 phase_ref_sc = "SELF_REF"; /*we are robust to phase_ref_sc=NONE but SELF_REF is better */
1933 cpl_msg_info(cpl_func, "Reference phase for SC forced to %s due to option SELF_VISPHI", phase_ref_sc);
1934 } else cpl_msg_info(cpl_func, "Reference phase for SC is %s", phase_ref_sc);
1935 } else cpl_msg_info(cpl_func, "Reference phase for SC is %s", phase_ref_sc);
1936
1937 cpl_msg_info (cpl_func, "Output phase for SC is %s",output_phase_sc);
1938
1939 /* Other reduction parameters */
1940 int v_factor_flag_sc = strstr (gravi_param_get_string (parlist, "gravity.vis.vis-correction-sc"),"VFACTOR") ? 1 : 0;
1941 int p_factor_flag_sc = strstr (gravi_param_get_string (parlist, "gravity.vis.vis-correction-sc"),"PFACTOR") ? 1 : 0;
1942 int debiasing_flag_sc = gravi_param_get_bool (parlist, "gravity.vis.debias-sc");
1943 int nboot_sc = gravi_param_get_int (parlist, "gravity.vis.nboot");
1944 const char* rangeString = gravi_param_get_string (parlist, "gravity.vis.output-phase-channels");
1945 double outlier_threshold_sc = gravi_param_get_double (parlist, "gravity.vis.outlier-fraction-threshold");
1946 cpl_msg_info (cpl_func, "Bias subtraction of V2 for SC is %s",debiasing_flag_sc?"ENABLE":"DISABLE");
1947 cpl_msg_info (cpl_func, "Threshold for fraction of outlier is %.3f",outlier_threshold_sc);
1948 /*
1949 force VFACTOR and PFACTOR to 0 for SELF_VISPHI by precaution.
1950 */
1951 if (!strcmp(output_phase_sc, "SELF_VISPHI")) {
1952 v_factor_flag_sc= 0;
1953 p_factor_flag_sc= 0;
1954 cpl_msg_info(cpl_func, "vFactor correction for SC is %s due to option SELF_VISPHI", v_factor_flag_sc ? "ENABLE" : "DISABLE");
1955 cpl_msg_info(cpl_func, "pFactor correction for SC is %s due to option SELF_VISPHI", p_factor_flag_sc ? "ENABLE" : "DISABLE");
1956 } else {
1957 cpl_msg_info (cpl_func, "vFactor correction for SC is %s",v_factor_flag_sc?"ENABLE":"DISABLE");
1958 cpl_msg_info (cpl_func, "pFactor correction for SC is %s",p_factor_flag_sc?"ENABLE":"DISABLE");
1959 }
1960
1961 CPLCHECK_NUL("Cannot get parameters");
1962
1963 /*
1964 * Loop on polarisations
1965 */
1966 for (int pol = 0; pol < npol_sc; pol++) {
1967 cpl_msg_info (cpl_func, "Start SC polarisation %d over %d",pol+1, npol_sc);
1968
1969 /* Get the input table of SC */
1970 cpl_table * vis_SC = gravi_data_get_oi_vis (p2vmred_data, GRAVI_SC, pol, npol_sc);
1971 cpl_table * flux_SC = gravi_data_get_oi_flux (p2vmred_data, GRAVI_SC, pol, npol_sc);
1972 cpl_table * oi_wavelengthsc = gravi_data_get_oi_wave (p2vmred_data, GRAVI_SC, pol, npol_sc);
1973 CPLCHECK_NUL ("Cannot get data");
1974
1975 /* Compute the wavenumber for SC in [m^-1] */
1976 cpl_array * wavenumber_sc;
1977 int nwave_sc = cpl_table_get_column_depth (vis_SC, "VISDATA");
1978 wavenumber_sc = cpl_array_new (nwave_sc, CPL_TYPE_DOUBLE);
1979 for (cpl_size wave = 0; wave < nwave_sc; wave ++){
1980 cpl_array_set (wavenumber_sc, wave, 1./cpl_table_get (oi_wavelengthsc, "EFF_WAVE", wave, &nv));
1981 }
1982
1983 CPLCHECK_NUL ("Cannot build the wave and wavenumber");
1984
1985 /* Create averaged tables */
1986 cpl_table * oi_vis2_SC = gravi_table_oi_create (nwave_sc, 1, GRAVI_OI_VIS2_EXT);
1987 gravi_table_new_column (oi_vis2_SC, "NDIT", NULL, CPL_TYPE_INT);
1988 gravi_table_new_column (oi_vis2_SC, "NVALID", NULL, CPL_TYPE_INT);
1989
1990 cpl_table * oi_vis_SC = gravi_table_oi_create (nwave_sc, 1, GRAVI_OI_VIS_EXT);
1991 gravi_table_new_column (oi_vis_SC, "NDIT", NULL, CPL_TYPE_INT);
1992 gravi_table_new_column (oi_vis_SC, "NVALID", NULL, CPL_TYPE_INT);
1993 gravi_table_new_column (oi_vis_SC, "GDELAY", "m", CPL_TYPE_DOUBLE);
1994 gravi_table_new_column (oi_vis_SC, "PHASE", "rad", CPL_TYPE_DOUBLE);
1995
1996 cpl_table * oi_T3_SC = gravi_table_oi_create (nwave_sc, 1, GRAVI_OI_T3_EXT);
1997 gravi_table_new_column (oi_T3_SC, "NDIT", NULL, CPL_TYPE_INT);
1998 gravi_table_new_column (oi_T3_SC, "NVALID", NULL, CPL_TYPE_INT);
1999
2000 cpl_table * oi_flux_SC = gravi_table_oi_create (nwave_sc, 1, GRAVI_OI_FLUX_EXT);
2001 gravi_table_new_column (oi_flux_SC, "NDIT", NULL, CPL_TYPE_INT);
2002 gravi_table_new_column (oi_flux_SC, "NVALID", NULL, CPL_TYPE_INT);
2003 gravi_table_new_column (oi_flux_SC, "LKDT_MET_FC", "mjd", CPL_TYPE_DOUBLE);
2004
2005 CPLCHECK_NUL("Cannot create columns in averaged OIFITS...");
2006
2007 /* Keep only selected rows */
2008 vis_SC = gravi_table_extract_time_interval (vis_SC, start_time, end_time);
2009 flux_SC = gravi_table_extract_time_interval (flux_SC, start_time, end_time);
2010
2011 /*
2012 * Compute OIVIS2 and OIVIS for SC
2013 */
2014 cpl_msg_info (cpl_func, "Compute OIVIS2 and OIVIS for SC");
2015
2016 gravi_vis_average_bootstrap (oi_vis_SC, oi_vis2_SC, vis_SC,
2017 nboot_sc,
2018 phase_ref_sc,
2019 v_factor_flag_sc,
2020 p_factor_flag_sc,
2021 debiasing_flag_sc,
2022 outlier_threshold_sc);
2023 CPLCHECK_NUL("Cannot average the SC frames");
2024
2025 /* Compute other columns */
2026 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "OPD_MET_FC", 6);
2027 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "PHASE_REF_COEFF", 6);
2028 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "E_U", 6);
2029 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "E_V", 6);
2030 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "E_W", 6);
2031 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "E_AZ", 6);
2032 gravi_vis_compute_column_mean (oi_vis_SC, vis_SC, "E_ZD", 6);
2033 CPLCHECK_NUL("Cannot compute means.");
2034
2035 /* Re compute the astrometric phase from VISDATA to deal with absolute phase
2036 * VISDATA as well as (R,I) remains unchanged. The goal is to split
2037 * the differential phase, calibratable so far, from the absolute phase */
2038 if ( !strcmp (output_phase_sc,"DIFFERENTIAL") || !strcmp (output_phase_sc,"ABSOLUTE") ) {
2039 for (int base = 0; base < nbase; base++) {
2040
2041 /* We duplicate VISDATA, to keep the value untouched in the table */
2042 cpl_array * visData_sc, * visErr_sc;
2043 visData_sc = cpl_array_cast (cpl_table_get_array (oi_vis_SC, "VISDATA", base),
2044 CPL_TYPE_DOUBLE_COMPLEX);
2045
2046 /* Normalize the phasor by error, to discard crazy points */
2047 visErr_sc = cpl_array_duplicate (visData_sc);
2048 cpl_array_abs (visErr_sc);
2049 cpl_array_divide (visData_sc, visErr_sc);
2050
2051 /* Get the flag */
2052 cpl_array * flag_sc;
2053 flag_sc = (cpl_array *)cpl_table_get_array (oi_vis_SC, "FLAG", base);
2054
2055 /* Compute and remove the mean group delay in [m] */
2056 double mean_delay = 0.0;
2057 gravi_array_get_group_delay_loop (&visData_sc, &flag_sc, wavenumber_sc, &mean_delay, 1, 2e-3, CPL_FALSE);
2058 gravi_array_multiply_phasor (visData_sc, - 2*I*CPL_MATH_PI * mean_delay, wavenumber_sc);
2059
2060 /* Save this delay [m] */
2061 cpl_table_set (oi_vis_SC, "GDELAY", base, mean_delay);
2062
2063 /* Compute and remove the mean phase in [rad] */
2064 double mean_phase = carg (cpl_array_get_mean_complex (visData_sc));
2065 cpl_array_multiply_scalar_complex (visData_sc, cexp(- I * mean_phase));
2066
2067 /* Save this phase [rad] */
2068 cpl_table_set (oi_vis_SC, "PHASE", base, mean_phase);
2069
2070 /* Set back the phase in [deg] (skip for ABSOLUTE mode) */
2071 if ( !strcmp (output_phase_sc,"DIFFERENTIAL") ) {
2072 cpl_array_arg (visData_sc);
2073 gravi_table_set_array_phase (oi_vis_SC, "VISPHI", base, visData_sc);
2074 }
2075 cpl_array_delete (visData_sc);
2076 cpl_array_delete (visErr_sc);
2077
2078 CPLCHECK_NUL("when computing the astrometric phase");
2079
2080 } /* End loop on base */
2081 }
2082 if (!strcmp(output_phase_sc, "SELF_VISPHI")) {
2083 int* cmin=NULL;
2084 int* cmax=NULL;
2085 int nrange=0;
2086 /* rather complex C way to analyse strings defining clusters of wavelengths like " [ 12345 : 12346 , 678 : 680 , 822:864]" */
2087 if (strcmp(rangeString, "UNKNOWN")) {
2088 /*find number of ranges (they are separated by ',')*/
2089 char *str, *str1 ;
2090 int l=strlen(rangeString)+1;
2091 int j=0;
2092 int i=0;
2093 str=(char*)malloc(l);
2094 strncpy(str,rangeString,l); /*for future use*/
2095 for (i = 0; i<l; ++i) if (str[i]!=' ' && str[i]!='\t') str[j++]=str[i]; //remove ALL blanks.
2096 str[j]='\0';
2097 l=strlen(str)+1;
2098 str1=(char*)malloc(l);
2099 strncpy(str1,str,l); /*for future use, as strtok destroys its arguments*/
2100
2101 char *token;
2102 token = strtok(str, "[,]");
2103 while (token) {
2104 nrange++;
2105 token = strtok(NULL, "[,]");
2106 }
2107 if (nrange > 1) {
2108 cmin=(int*) calloc(nrange,sizeof(int));
2109 cmax=(int*) calloc(nrange,sizeof(int));
2110
2111 char *str2, *subtoken;
2112 char *saveptr1, *saveptr2;
2113 for (j = 0; ; j++, str1 = NULL) {
2114 token = strtok_r(str1, "[,]" , &saveptr1);
2115 if (token == NULL)
2116 break;
2117 for (str2 = token, i=0; i<2 ; str2 = NULL, ++i) {
2118 subtoken = strtok_r(str2, ":", &saveptr2);
2119 if (subtoken == NULL)
2120 break;
2121 /* int ret=sscanf(subtoken,"%d", (i==0)?&(cmin[j]):&(cmax[j])); */
2122 }
2123 }
2124 }
2125 }
2126
2127 gravi_average_self_visphi(oi_vis_SC, vis_SC, wavenumber_sc, phase_ref_sc, cmin, cmax, nrange);
2128 }
2129 /*
2130 * Compute OIT3 for SC
2131 */
2132 cpl_msg_info (cpl_func, "Compute OIT3 for SC");
2133
2134 gravi_t3_average_bootstrap (oi_T3_SC, vis_SC, flux_SC,
2135 nboot_sc,
2136 v_factor_flag_sc,
2137 p_factor_flag_sc,
2138 outlier_threshold_sc);
2139 CPLCHECK_NUL("Cannot average t3 of SC");
2140
2141 /*
2142 * Compute OI_FLUX for SC
2143 */
2144 cpl_msg_info (cpl_func, "Compute OI_FLUX for SC");
2145
2146 gravi_flux_average_bootstrap (oi_flux_SC, flux_SC,
2147 nboot_sc, outlier_threshold_sc);
2148 CPLCHECK_NUL("Cannot average flux of SC");
2149
2150 /* Compute other columns */
2151 gravi_vis_compute_column_mean (oi_flux_SC, flux_SC, "OPD_MET_FC", 4);
2152 gravi_vis_compute_column_mean (oi_flux_SC, flux_SC, "FT_POS", 4);
2153 gravi_vis_compute_column_mean (oi_flux_SC, flux_SC, "SC_POS", 4);
2154 gravi_vis_compute_column_mean (oi_flux_SC, flux_SC, "OPL_AIR", 4);
2155 CPLCHECK_NUL ("Cannot compute mean columns");
2156
2157 /* Save the FC metrology lock date */
2158 for (int tel = 0; tel < ntel; tel++){
2159 double lockdate = gravi_pfits_get_metfc_lockmjd (p2vmred_header, tel);
2160 cpl_table_set (oi_flux_SC, "LKDT_MET_FC", tel, lockdate);
2161 }
2162
2163 /*
2164 * Add tables in the vis_data
2165 */
2166 cpl_propertylist * vis_plist = gravi_data_get_oi_vis_plist (p2vmred_data, GRAVI_SC, pol, npol_sc);
2167 cpl_propertylist * oivis_plist = cpl_propertylist_new();
2168 cpl_propertylist_copy_property (oivis_plist, vis_plist, "DATE-OBS");
2169 cpl_propertylist_copy_property (oivis_plist, vis_plist, "EXTVER");
2170 cpl_propertylist_copy_property (oivis_plist, vis_plist, "ARRNAME");
2171 cpl_propertylist_copy_property (oivis_plist, vis_plist, "INSNAME");
2172 cpl_propertylist_update_string (oivis_plist, "AMPTYP","absolute");
2173 if ( !strcmp (output_phase_sc,"DIFFERENTIAL") )
2174 cpl_propertylist_update_string (oivis_plist, "PHITYP","differential");
2175 if ( !strcmp (output_phase_sc,"ABSOLUTE") )
2176 cpl_propertylist_update_string (oivis_plist, "PHITYP","absolute");
2177 cpl_propertylist_update_int (oivis_plist, "PHIORDER",1);
2178 gravi_data_add_table (vis_data, oivis_plist, GRAVI_OI_VIS_EXT, oi_vis_SC);
2179
2180 cpl_propertylist * oivis2_plist = cpl_propertylist_new();
2181 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "DATE-OBS");
2182 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "EXTVER");
2183 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "ARRNAME");
2184 cpl_propertylist_copy_property (oivis2_plist, vis_plist, "INSNAME");
2185 gravi_data_add_table (vis_data, oivis2_plist, GRAVI_OI_VIS2_EXT, oi_vis2_SC);
2186
2187 cpl_propertylist * oit3_plist = cpl_propertylist_new();
2188 cpl_propertylist_copy_property (oit3_plist, vis_plist, "DATE-OBS");
2189 cpl_propertylist_copy_property (oit3_plist, vis_plist, "EXTVER");
2190 cpl_propertylist_copy_property (oit3_plist, vis_plist, "ARRNAME");
2191 cpl_propertylist_copy_property (oit3_plist, vis_plist, "INSNAME");
2192 gravi_data_add_table (vis_data, oit3_plist, GRAVI_OI_T3_EXT, oi_T3_SC);
2193
2194 cpl_propertylist * oiflux_plist = cpl_propertylist_new();
2195 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "DATE-OBS");
2196 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "EXTVER");
2197 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "ARRNAME");
2198 cpl_propertylist_copy_property (oiflux_plist, vis_plist, "INSNAME");
2199 cpl_propertylist_update_string (oiflux_plist, "CALSTAT", "U");
2200 cpl_propertylist_set_comment (oiflux_plist, "CALSTAT", "Uncalibrated flux per telescope");
2201 gravi_data_add_table (vis_data, oiflux_plist, GRAVI_OI_FLUX_EXT, oi_flux_SC);
2202
2203 CPLCHECK_NUL ("Cannot add tables");
2204
2205 /* Delete waves */
2206 FREE (cpl_array_delete, wavenumber_sc);
2207 CPLCHECK_NUL ("Cannot delete wavenumber");
2208
2209 FREE (cpl_table_delete, vis_SC);
2210 FREE (cpl_table_delete, flux_SC);
2211
2212 } /* end loop on pol */
2213 } /* End SC */
2214
2215
2216 /* Add the night-obs in the main HEADER. This is the MJD of the begining
2217 of the night, similar for all files from noon to noon (~local time) */
2218 double mjd_obs = cpl_table_get_column_mean (gravi_data_get_table (vis_data, GRAVI_OI_VIS_EXT), "MJD");
2219 cpl_propertylist_update_int (vis_header, GRAVI_NIGHT_OBS, (int)floor(mjd_obs-0.625));
2220
2222 return vis_data;
2223}
2224
2225
2226/*----------------------------------------------------------------------------*/
2233/*----------------------------------------------------------------------------*/
2234
2235cpl_error_code gravi_compute_vis_qc (gravi_data * vis_data, cpl_frameset* frameset)
2236{
2238 cpl_ensure_code (vis_data, CPL_ERROR_NULL_INPUT);
2239
2240 int nv, nbase = 6, ntel=4, nclo=4;
2241 char qc_name[100];
2242
2243 /*
2244 * Prepare the output
2245 */
2246
2247 cpl_propertylist * vis_header = gravi_data_get_header (vis_data);
2248 cpl_propertylist * plist = gravi_data_get_extra_primary_header (vis_data);
2249
2250
2251 /*
2252 * Start with FT
2253 */
2254 if (gravi_data_has_type (vis_data, "_FT") <= 0 ) {
2255 cpl_msg_info (cpl_func, "VIS data has no FT extensions");
2256 }
2257 else {
2258
2259 /* Loop on polarisations */
2260 int npol_ft = gravi_pfits_get_pola_num (vis_header, GRAVI_FT);
2261 for (int pol = 0; pol < npol_ft; pol++) {
2262 cpl_msg_info (cpl_func, "Start FT polarisation %d over %d",pol+1, npol_ft);
2263
2264 /* Loop on bases to compute OIVIS2 and OIVIS for FT
2265 */
2266 cpl_msg_info (cpl_func, "Compute QC OIVIS2 and OIVIS for FT");
2267
2268 cpl_table * oi_vis2_FT = gravi_data_get_oi_vis2 (vis_data, GRAVI_FT, pol, npol_ft);
2269 cpl_table * oi_vis_FT = gravi_data_get_oi_vis (vis_data, GRAVI_FT, pol, npol_ft);
2270
2271 for (int base = 0; base < nbase; base++) {
2272
2273 /* Add the QC parameters for FT */
2274
2275 sprintf (qc_name, "ESO QC VISPHIERR_FT%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2276 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_FT, "VISPHIERR", base, nbase));
2277 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2278
2279 sprintf (qc_name, "ESO QC VIS2_FT%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2280 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis2_FT, "VIS2DATA", base, nbase));
2281 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2282
2283 sprintf (qc_name, "ESO QC VIS2ERR_FT%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2284 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis2_FT, "VIS2ERR", base, nbase));
2285 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2286
2287 sprintf (qc_name, "ESO QC VISAMP_FT%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2288 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_FT, "VISAMP", base, nbase));
2289 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2290
2291 sprintf (qc_name, "ESO QC VISAMPERR_FT%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2292 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_FT, "VISAMPERR", base, nbase));
2293 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2294
2295 CPLCHECK_MSG("Cannot compute QC parameter for OI_VIS for FT");
2296 } /* End loop on base */
2297
2298 /*
2299 * Loop on triplet to compute OIT3 for FT
2300 */
2301 cpl_msg_info (cpl_func, "Compute QC OIT3 for FT");
2302
2303 cpl_table * oi_T3_FT = gravi_data_get_oi_t3 (vis_data, GRAVI_FT, pol, npol_ft);
2304
2305 for (int clo = 0; clo < nclo; clo++){
2306
2307 sprintf (qc_name, "ESO QC T3PHI_FT%s_P%d AVG", GRAVI_CLO_NAME[clo], pol+1);
2308 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_T3_FT, "T3PHI", clo, nclo));
2309 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2310
2311 sprintf (qc_name, "ESO QC T3PHIERR_FT%s_P%d AVG", GRAVI_CLO_NAME[clo], pol+1);
2312 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_T3_FT, "T3PHIERR", clo, nclo));
2313 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2314
2315 CPLCHECK_MSG("Cannot compute QC parameter for OI_T3 for FT");
2316 } /* End loop on triplets */
2317
2318 /*
2319 * Loop on beams to compute OI_FLUX for FT
2320 */
2321 cpl_msg_info (cpl_func, "Compute QC OI_FLUX for FT");
2322
2323 cpl_table * oi_flux_FT = gravi_data_get_oi_flux (vis_data, GRAVI_FT, pol, npol_ft);
2324
2325 for (int tel = 0; tel < ntel; tel++){
2326
2327 sprintf (qc_name, "ESO QC FLUX_FT%d_P%d AVG", tel+1, pol+1);
2328 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_flux_FT, "FLUX", tel, ntel));
2329 cpl_propertylist_set_comment (plist, qc_name, "[e/total_int_time] mean over lbd");
2330
2331 sprintf (qc_name, "ESO QC FLUXERR_FT%d_P%d AVG", tel+1, pol+1);
2332 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_flux_FT, "FLUXERR", tel, ntel));
2333 cpl_propertylist_set_comment (plist, qc_name, "[e/total_int_time] mean over lbd");
2334
2335 sprintf (qc_name, "ESO QC FLUXRATE_FT%d_P%d SUM", tel+1, pol+1);
2336 double flux_rate = cpl_array_get_mean (cpl_table_get_array (oi_flux_FT, "FLUX", tel)) *
2337 cpl_array_get_size (cpl_table_get_array (oi_flux_FT, "FLUX", tel)) / cpl_table_get_double (oi_flux_FT, "INT_TIME", tel, &nv);
2338 cpl_propertylist_update_double (plist, qc_name, flux_rate);
2339 cpl_propertylist_set_comment (plist, qc_name, "[e/s] sum over lbd");
2340
2341 CPLCHECK_MSG("Cannot compute QC parameter for OI_FLUX for FT");
2342 } /* End loop on beams */
2343
2344 } /* end loop on pol */
2345 } /* End FT */
2346
2347
2348
2349 /*
2350 * Then with SC
2351 */
2352 if (gravi_data_has_type (vis_data, "_SC") <= 0 ) {
2353 cpl_msg_info (cpl_func, "VIS data has no SC extensions");
2354 }
2355 else {
2356
2357 /* Loop on polarisations */
2358 int npol_sc = gravi_pfits_get_pola_num (vis_header, GRAVI_SC);
2359
2360 for (int pol = 0; pol < npol_sc; pol++) {
2361
2362 /*
2363 * Loop on bases to compute OIVIS2 and OIVIS for SC
2364 */
2365 cpl_msg_info (cpl_func, "Compute QC OIVIS2 and OIVIS for SC");
2366
2367 cpl_table * oi_vis2_SC = gravi_data_get_oi_vis2 (vis_data, GRAVI_SC, pol, npol_sc);
2368 cpl_table * oi_vis_SC = gravi_data_get_oi_vis (vis_data, GRAVI_SC, pol, npol_sc);
2369
2370 for (int base = 0; base < nbase; base++) {
2371 /* FIXME: repair these QC parameters, for instance by computing them in P2VMRED */
2372
2373 // sprintf (qc_name, "ESO QC VFACTOR%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2374 // double vmean = gravi_table_get_column_mean (vis_SC, "V_FACTOR_WL", base, nbase);
2375 // cpl_propertylist_update_double (plist, qc_name, vmean);
2376 // cpl_propertylist_set_comment (plist, qc_name, "mean v-factor");
2377 //
2378 // sprintf (qc_name, "ESO QC PFACTOR%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2379 // double pmean = gravi_table_get_column_mean (vis_SC, "P_FACTOR", base, nbase);
2380 // cpl_propertylist_update_double (plist, qc_name, pmean);
2381 // cpl_propertylist_set_comment (plist, qc_name, "mean p-factor");
2382
2383 sprintf (qc_name, "ESO QC GD_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2384 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_SC, "GDELAY", base, nbase));
2385 cpl_propertylist_set_comment (plist, qc_name, "[m] mean Group-Delay");
2386
2387 sprintf (qc_name, "ESO QC VIS2_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2388 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis2_SC, "VIS2DATA", base, nbase));
2389 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2390
2391 sprintf (qc_name, "ESO QC VIS2ERR_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2392 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis2_SC, "VIS2ERR", base, nbase));
2393 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2394
2395 sprintf (qc_name, "ESO QC VISPHI_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2396 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_SC, "VISPHI", base, nbase));
2397 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2398
2399 sprintf (qc_name, "ESO QC VISPHIERR_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2400 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_SC, "VISPHIERR", base, nbase));
2401 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2402
2403 sprintf (qc_name, "ESO QC VISAMP_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2404 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_SC, "VISAMP", base, nbase));
2405 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2406
2407 sprintf (qc_name, "ESO QC VISAMPERR_SC%s_P%d AVG", GRAVI_BASE_NAME[base], pol+1);
2408 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_vis_SC, "VISAMPERR", base, nbase));
2409 cpl_propertylist_set_comment (plist, qc_name, "mean over lbd");
2410
2411 double coeff2 = gravi_table_get_value (oi_vis_SC, "PHASE_REF_COEFF", base, 2);
2412 sprintf (qc_name, "ESO QC PHASE_REF_COEFF2 SC%s_P%d", GRAVI_BASE_NAME[base], pol+1);
2413 cpl_propertylist_update_double (plist, qc_name, coeff2);
2414 cpl_propertylist_set_comment (plist, qc_name, "[rad] 2sd order of FT phase");
2415
2416 CPLCHECK_MSG("Cannot set QC parameter for OI_VIS for SC");
2417 } /* End loop on base */
2418
2419 /*
2420 * Loop on triplet to compute OIT3 for SC
2421 */
2422 cpl_msg_info (cpl_func, "Compute QC OIT3 for SC");
2423
2424 cpl_table * oi_T3_SC = gravi_data_get_oi_t3 (vis_data, GRAVI_SC, pol, npol_sc);
2425
2426 for (int clo = 0; clo < nclo; clo++){
2427
2428 sprintf (qc_name, "ESO QC T3PHI_SC%s_P%d AVG", GRAVI_CLO_NAME[clo], pol+1);
2429 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_T3_SC, "T3PHI", clo, nclo));
2430 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2431
2432 sprintf (qc_name, "ESO QC T3PHIERR_SC%s_P%d AVG", GRAVI_CLO_NAME[clo], pol+1);
2433 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_T3_SC, "T3PHIERR", clo, nclo));
2434 cpl_propertylist_set_comment (plist, qc_name, "[deg] mean over lbd");
2435
2436 CPLCHECK_MSG("Cannot set QC parameter for OI_T3 for SC");
2437 }/* End loop on triplets */
2438
2439 /*
2440 * Loop on beams to compute OI_FLUX for SC
2441 */
2442 cpl_msg_info (cpl_func, "Compute QC OI_FLUX for SC");
2443
2444 cpl_table * oi_flux_SC = gravi_data_get_oi_flux (vis_data, GRAVI_SC, pol, npol_sc);
2445
2446 for (int tel = 0; tel < ntel; tel++){
2447
2448 sprintf (qc_name, "ESO QC FLUX_SC%d_P%d AVG", tel+1, pol+1);
2449 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_flux_SC, "FLUX", tel, ntel));
2450 cpl_propertylist_set_comment (plist, qc_name, "[e/total_int_time] mean over lbd");
2451
2452 sprintf (qc_name, "ESO QC FLUXERR_SC%d_P%d AVG", tel+1, pol+1);
2453 cpl_propertylist_update_double (plist, qc_name, gravi_table_get_column_mean (oi_flux_SC, "FLUXERR", tel, ntel));
2454 cpl_propertylist_set_comment (plist, qc_name, "[e/total_int_time] mean over lbd");
2455
2456 sprintf (qc_name, "ESO QC FLUXRATE_SC%d_P%d SUM", tel+1, pol+1);
2457 double flux_rate = cpl_array_get_mean (cpl_table_get_array (oi_flux_SC, "FLUX", tel)) *
2458 cpl_array_get_size(cpl_table_get_array (oi_flux_SC, "FLUX", tel)) / cpl_table_get_double (oi_flux_SC, "INT_TIME", tel, &nv);
2459 cpl_propertylist_update_double (plist, qc_name, flux_rate);
2460 cpl_propertylist_set_comment (plist, qc_name, "[e/s] sum over lbd");
2461
2462 double ftpos_mean = cpl_table_get (oi_flux_SC, "FT_POS", tel, NULL);
2463 sprintf (qc_name, "ESO QC FT_POS SC%d_P%d", tel+1, pol+1);
2464 cpl_propertylist_update_double (plist, qc_name, ftpos_mean);
2465 cpl_propertylist_set_comment (plist, qc_name, "[V]");
2466
2467 double oplair_mean = cpl_table_get (oi_flux_SC, "OPL_AIR", tel, NULL);
2468 sprintf (qc_name, "ESO QC OPL_AIR SC%d_P%d", tel+1, pol+1);
2469 cpl_propertylist_update_double (plist, qc_name, oplair_mean);
2470 cpl_propertylist_set_comment (plist, qc_name, "[m]");
2471
2472 CPLCHECK_MSG("Cannot set QC parameter for OI_FLUX for SC");
2473 } /* End loop on beams */
2474
2475 } /* end loop on pol */
2476
2477 cpl_msg_info (cpl_func, "Compute IDP parameters");
2478
2479 /* Compute additional idp parameters */
2480 cpl_propertylist * idp_hdr = gravi_idp_compute(vis_data, vis_header, frameset);
2481 cpl_propertylist_append(plist, idp_hdr);
2482 cpl_propertylist_delete(idp_hdr);
2483
2484 } /* End SC */
2485
2486
2487 cpl_propertylist_update_string (plist, "ESO QC FIELD MODE",
2488 gravi_pfits_get_mode_name(vis_header));
2489 cpl_propertylist_set_comment (plist, "ESO QC FIELD MODE", "Field mode");
2490
2491 CPLCHECK_MSG("Cannot create QC parameters");
2492
2494 return CPL_ERROR_NONE;
2495}
2496
2497/*----------------------------------------------------------------------------*/
2510cpl_error_code gravi_data_get_minmax_uvcoord(const cpl_table *oi_vis2,
2511 double * min_uvcoord,
2512 double * max_uvcoord)
2513{
2514 cpl_ensure (oi_vis2, CPL_ERROR_NULL_INPUT, 0.0);
2515
2516 *min_uvcoord = DBL_MAX;
2517 *max_uvcoord = DBL_MIN;
2518
2519 int valid;
2520 cpl_size nrow = cpl_table_get_nrow (oi_vis2);
2521
2522 const double * ucoord = cpl_table_get_data_double_const(oi_vis2, "UCOORD");
2523 const double * vcoord = cpl_table_get_data_double_const(oi_vis2, "VCOORD");
2524
2525 const cpl_array ** flags = cpl_table_get_data_array_const (oi_vis2, "FLAG");
2526
2527 double uvcoord = 0;
2528 cpl_size flag_array_size = cpl_array_get_size(flags[0]);
2529 for (cpl_size r=0; r<nrow;r++)
2530 {
2531 int flagged = 0;
2532 for(cpl_size el=0; el<flag_array_size; el++)
2533 {
2534 if (cpl_array_get_int(flags[r], el, &valid))
2535 {
2536 flagged = 1;
2537 break;
2538 }
2539 }
2540 if(!flagged)
2541 {
2542 uvcoord = sqrt(ucoord[r]*ucoord[r]+vcoord[r]*vcoord[r]);
2543 if(uvcoord > *max_uvcoord)
2544 *max_uvcoord = uvcoord;
2545 if(uvcoord < *min_uvcoord)
2546 *min_uvcoord = uvcoord;
2547 }
2548 }
2549 return CPL_ERROR_NONE;
2550}
2551
2552
2553
2554/*----------------------------------------------------------------------------*/
2563/*----------------------------------------------------------------------------*/
2564
2565cpl_error_code gravi_normalize_sc_to_ft (gravi_data * vis_data)
2566{
2568 cpl_ensure_code (vis_data, CPL_ERROR_NULL_INPUT);
2569
2570 cpl_propertylist * hdr_data = gravi_data_get_header (vis_data);
2571 int pol, npol = gravi_pfits_get_pola_num (hdr_data, GRAVI_SC);
2572 double qFactor;
2573
2574 if ( npol != gravi_pfits_get_pola_num (hdr_data, GRAVI_FT)) {
2575 return cpl_error_set_message(cpl_func,CPL_ERROR_ILLEGAL_INPUT,"polarisation of SC and FT shall be compatible");
2576 }
2577
2578 /* Loop on polarisation. Assume the same polarisation
2579 * splitting for both SC and FT */
2580 for ( pol= 0 ; pol < npol ; pol++ ) {
2581
2582 cpl_table * oi_wave_sc = gravi_data_get_oi_wave (vis_data, GRAVI_SC, pol, npol);
2583 cpl_table * oi_wave_ft = gravi_data_get_oi_wave (vis_data, GRAVI_FT, pol, npol);
2584
2585 /*
2586 * Get data for VIS2 and VISAMP
2587 */
2588 cpl_table * oi_vis2_sc = gravi_data_get_oi_vis2 (vis_data, GRAVI_SC, pol, npol);
2589 cpl_table * oi_vis2_ft = gravi_data_get_oi_vis2 (vis_data, GRAVI_FT, pol, npol);
2590 cpl_table * oi_vis_sc = gravi_data_get_oi_vis (vis_data, GRAVI_SC, pol, npol);
2591 cpl_table * oi_vis_ft = gravi_data_get_oi_vis (vis_data, GRAVI_FT, pol, npol);
2592
2593 CPLCHECK_MSG("Cannot get data");
2594
2595 /* Loop on baselines */
2596 for (cpl_size base = 0; base < cpl_table_get_nrow (oi_vis2_ft); base ++) {
2597
2598 /* Get the VIS2 of FT */
2599 const cpl_array * vis2_ft = cpl_table_get_array (oi_vis2_ft, "VIS2DATA", base);
2600
2601 /* Create the rebin VIS2 of SC */
2602 cpl_array * vis2_lr = gravi_array_rebin (cpl_table_get_array (oi_vis2_sc, "VIS2DATA", base),
2603 cpl_table_get_array (oi_vis2_sc, "VIS2ERR", base),
2604 oi_wave_sc, oi_wave_ft);
2605
2606 /* Compute the mean visibility loss over the band.
2607 * FIXME: shall use vis2_ft = (a.lbd+b) * vis2_lr, which could be done with cpl_matrix */
2608 qFactor = cpl_array_get_mean (vis2_lr) / cpl_array_get_mean (vis2_ft);
2609 cpl_msg_info (cpl_func, "vis2 %lli: qFactor = %f", base, qFactor);
2610
2611 /* Divide the SC data */
2612 cpl_array_divide_scalar (cpl_table_get_data_array (oi_vis2_sc, "VIS2DATA")[base], qFactor);
2613 cpl_array_divide_scalar (cpl_table_get_data_array (oi_vis2_sc, "VIS2ERR")[base], qFactor);
2614
2615 /* Get the VISAMP of FT */
2616 const cpl_array * vis_ft = cpl_table_get_array (oi_vis_ft, "VISAMP", base);
2617
2618 /* Create the rebin VISAMP of SC */
2619 cpl_array * vis_lr = gravi_array_rebin (cpl_table_get_array (oi_vis_sc, "VISAMP", base),
2620 cpl_table_get_array (oi_vis_sc, "VISAMPERR", base),
2621 oi_wave_sc, oi_wave_ft);
2622
2623 /* Compute the mean visibility loss over the band. */
2624 qFactor = cpl_array_get_mean (vis_lr) / cpl_array_get_mean (vis_ft);
2625 cpl_msg_info (cpl_func, "visAmp %lli: qFactor = %f", base, qFactor);
2626
2627 /* Divide the SC data */
2628 cpl_array_divide_scalar (cpl_table_get_data_array (oi_vis_sc, "VISAMP")[base], qFactor);
2629 cpl_array_divide_scalar (cpl_table_get_data_array (oi_vis_sc, "VISAMPERR")[base], qFactor);
2630
2631 FREE (cpl_array_delete, vis2_lr);
2632 FREE (cpl_array_delete, vis_lr);
2633 } /* End loop on baselines */
2634
2635 } /* End loop on pol */
2636
2638 return CPL_ERROR_NONE;
2639}
2640
2641/*----------------------------------------------------------------------------*/
2649/*----------------------------------------------------------------------------*/
2650
2651cpl_error_code gravi_vis_mjd_to_time (gravi_data * vis_data)
2652{
2654 cpl_ensure_code (vis_data, CPL_ERROR_NULL_INPUT);
2655 char date[90];
2656
2657 /* Loop on extension */
2658 int next = gravi_data_get_size (vis_data);
2659 for (int ext = 0; ext < next; ext ++) {
2660
2661 const char * extname = gravi_data_get_extname (vis_data,ext);
2662 if (!strcmp (extname, "OI_VIS") ||
2663 !strcmp (extname, "OI_VIS2") ||
2664 !strcmp (extname, "OI_T3") ||
2665 !strcmp (extname, "OI_FLUX")) {
2666
2667 /* Get the DATE-OBS in format YYYY-MM-DDT00:00:00.000 */
2668 cpl_propertylist * plist = gravi_data_get_plist_x (vis_data, ext);
2669 sprintf (date, "%.10sT00:00:00.000", cpl_propertylist_get_string (plist, "DATE-OBS"));
2670
2671 /* Get the MJD of this DATE-OBS */
2672 double mjd0 = gravi_convert_to_mjd (date);
2673 cpl_msg_debug (cpl_func, "DATE-OBS = %s -> mjd = %.3f", date, mjd0);
2674
2675 /* Compute TIME in [s] following the OIFITS standard */
2676 cpl_table * oi_table = gravi_data_get_table_x (vis_data, ext);
2677 cpl_size nrow = cpl_table_get_nrow (oi_table);
2678 for (cpl_size row = 0; row < nrow; row++) {
2679 double mjd = cpl_table_get (oi_table, "MJD", row, NULL);
2680 cpl_table_set (oi_table, "TIME", row, (mjd-mjd0) * 24 * 3600);
2681 }
2682
2683 /* Set units */
2684 cpl_table_set_column_unit (oi_table, "TIME", "s");
2685 }
2686 } /* End loop on extensions */
2687
2689 return CPL_ERROR_NONE;
2690}
2691
2692
2693/*----------------------------------------------------------------------------*/
2703/*----------------------------------------------------------------------------*/
2704
2705cpl_error_code gravi_flat_flux (gravi_data * vis_data, gravi_data * p2vm_map)
2706{
2708 cpl_ensure_code (vis_data, CPL_ERROR_NULL_INPUT);
2709 cpl_ensure_code (p2vm_map, CPL_ERROR_NULL_INPUT);
2710
2711 int num_used_tf = 1;
2712 gravi_data **used_tf_data = &p2vm_map;
2713
2714 /* Get the header */
2715 cpl_propertylist * hdr_data = gravi_data_get_header (vis_data);
2716
2717 /* For each type of data SC / FT */
2718 int ntype_data = 2;
2719 for (int type_data = 0; type_data < ntype_data ; type_data ++) {
2720
2721 /* Loop on polarisation */
2722 int npol = gravi_pfits_get_pola_num (hdr_data, type_data);
2723 for (int pol= 0 ; pol < npol ; pol++ ) {
2724
2725 /* Calibrate the FLUX as a real quantity */
2726 double delta_t = 10000.0;
2727 gravi_apply_tf_amp (vis_data, NULL, used_tf_data, num_used_tf,
2729 GRAVI_INSNAME(type_data, pol, npol),
2730 "FLUX", "FLUXERR", 4, delta_t);
2731
2732 CPLCHECK_MSG("Cannot apply normalize flux");
2733
2734 }
2735 /* End loop on polarisation */
2736 }
2737 /* End loop on data_type */
2738
2740 return CPL_ERROR_NONE;
2741}
2742
2743/*----------------------------------------------------------------------------*/
2753/*----------------------------------------------------------------------------*/
2754
2755cpl_error_code gravi_vis_average_amp (cpl_table *oi_table, const char *name, const char *err, int nbase)
2756{
2757 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
2758 cpl_ensure_code (name, CPL_ERROR_NULL_INPUT);
2759 cpl_ensure_code (err, CPL_ERROR_NULL_INPUT);
2760
2761 cpl_size nwave = cpl_table_get_column_depth (oi_table, name);
2762 cpl_array * weight = gravi_array_init_double (nwave, 0.0);
2763 cpl_array * value = gravi_array_init_double (nwave, 0.0);
2764
2765 /* Loop on base */
2766 int nrow = cpl_table_get_nrow (oi_table) / nbase;
2767 for (cpl_size base = 0; base < nbase ; base++) {
2768 cpl_array_fill_window (weight, 0, nwave, 0.0);
2769 cpl_array_fill_window (value, 0, nwave, 0.0);
2770
2771 /* Loop on row and wave */
2772 for (cpl_size row = 0; row < nrow ; row++) {
2773 const cpl_array * rval = cpl_table_get_array (oi_table, name, base + row*nbase);
2774 const cpl_array * rerr = cpl_table_get_array (oi_table, err, base + row*nbase);
2775 const cpl_array * flag = cpl_table_get_array (oi_table, "FLAG", base + row*nbase);
2776 for (cpl_size wave = 0; wave < nwave; wave++) {
2777 double w = pow (cpl_array_get (rerr, wave, NULL), -2);
2778 if (cpl_array_get (flag, wave, NULL)) w = 10e-20;
2779 double v = cpl_array_get (rval, wave, NULL);
2780 cpl_array_set (weight, wave, cpl_array_get (weight, wave, NULL) + w);
2781 cpl_array_set (value, wave, cpl_array_get (value, wave, NULL) + v * w);
2782 }
2783 }
2784 CPLCHECK_MSG("Cannot average amp");
2785
2786 /* Set the mean */
2787 cpl_array_divide (value, weight);
2788 cpl_table_set_array (oi_table, name, base, value);
2789
2790 /* Set the variance of the mean */
2791 cpl_array_power (weight, -0.5);
2792 cpl_table_set_array (oi_table, err, base, weight);
2793
2794
2795
2796 } /* End loop on base */
2797
2798 FREE (cpl_array_delete, weight);
2799 FREE (cpl_array_delete, value);
2800 return CPL_ERROR_NONE;
2801}
2802
2803/*----------------------------------------------------------------------------*/
2814/*----------------------------------------------------------------------------*/
2815
2816cpl_error_code gravi_vis_average_phi (cpl_table *oi_table, const char *name, const char *err, int nbase)
2817{
2818 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
2819 cpl_ensure_code (name, CPL_ERROR_NULL_INPUT);
2820 cpl_ensure_code (err, CPL_ERROR_NULL_INPUT);
2821
2822 cpl_size nwave = cpl_table_get_column_depth (oi_table, name);
2823 cpl_array * weight = gravi_array_init_double (nwave, 0.0);
2824 cpl_array * value = gravi_array_init_double_complex (nwave, 0.0 + I*0.0);
2825
2826 /* Loop on base */
2827 int nrow = cpl_table_get_nrow (oi_table) / nbase;
2828 for (cpl_size base = 0; base < nbase ; base++) {
2829 cpl_array_fill_window (weight, 0, nwave, 0.0);
2830 cpl_array_fill_window_complex (value, 0, nwave, 0.0);
2831
2832 /* Loop on row and wave */
2833 for (cpl_size row = 0; row < nrow ; row++) {
2834 const cpl_array * rval = cpl_table_get_array (oi_table, name, base + row*nbase);
2835 const cpl_array * rerr = cpl_table_get_array (oi_table, err, base + row*nbase);
2836 const cpl_array * flag = cpl_table_get_array (oi_table, "FLAG", base + row*nbase);
2837 for (cpl_size wave = 0; wave < nwave; wave++) {
2838 double w = pow (cpl_array_get (rerr, wave, NULL), -2);
2839 if (cpl_array_get (flag, wave, NULL)) w = 10e-20;
2840 double complex v = cexp (1.*I * cpl_array_get (rval, wave, NULL) * CPL_MATH_RAD_DEG);
2841 cpl_array_set (weight, wave, cpl_array_get (weight, wave, NULL) + w);
2842 cpl_array_set_complex (value, wave, cpl_array_get_complex (value, wave, NULL) + v * w);
2843 }
2844 }
2845 CPLCHECK_MSG("Cannot average phi");
2846
2847 /* Set the mean */
2848 gravi_table_set_array_phase (oi_table, name, base, value);
2849 /* Set the variance of the mean */
2850 cpl_array_power (weight, -0.5);
2851 cpl_table_set_array (oi_table, err, base, weight);
2852
2853 } /* End loop on base */
2854
2855 FREE (cpl_array_delete, weight);
2856 FREE (cpl_array_delete, value);
2857 return CPL_ERROR_NONE;
2858}
2859
2860/*----------------------------------------------------------------------------*/
2870/*----------------------------------------------------------------------------*/
2871
2872cpl_error_code gravi_vis_average_value (cpl_table *oi_table, const char *name, const char *err, int nbase)
2873{
2874 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
2875 cpl_ensure_code (name, CPL_ERROR_NULL_INPUT);
2876 int nv = 0;
2877
2878 /* Loop on base */
2879 int nrow = cpl_table_get_nrow (oi_table) / nbase;
2880 for (cpl_size base = 0; base < nbase ; base++) {
2881 double weight = 0.0;
2882 double value = 0.0;
2883
2884 /* Loop on row */
2885 for (cpl_size row = 0; row < nrow ; row++) {
2886 double w = (err!=NULL ? pow (cpl_table_get (oi_table, err, base + row*nbase, &nv), -2.0) : 1.0);
2887 value += cpl_table_get (oi_table, name, base + row*nbase, &nv) * w;
2888 weight += w;
2889 }
2890 CPLCHECK_MSG("Cannot average value");
2891
2892 /* Set the mean */
2893 cpl_table_set (oi_table, name, base, value / weight);
2894 } /* End loop on base */
2895
2896 return CPL_ERROR_NONE;
2897}
2898
2899/*----------------------------------------------------------------------------*/
2908/*----------------------------------------------------------------------------*/
2909cpl_error_code gravi_force_uncertainties (gravi_data * oi_data,
2910 const cpl_parameterlist * parlist)
2911{
2913 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
2914 cpl_ensure_code (parlist, CPL_ERROR_NULL_INPUT);
2915
2916 double err;
2917
2918 /* Get header */
2919 cpl_propertylist * header = gravi_data_get_header (oi_data);
2920
2921 /* VISAMPERR SC */
2922 err = gravi_param_get_double_default (parlist, "gravity.postprocess.visamperr-sc", -1.0);
2923 if ( err > 0) {
2924 cpl_msg_info (cpl_func,"Force VISAMPERR to %.e for all observations", err);
2925
2927 for (int pol = 0; pol < npol; pol++) {
2928 cpl_table * oi_table = gravi_data_get_oi_vis (oi_data, GRAVI_SC, pol, npol);
2929 cpl_array ** array = cpl_table_get_data_array (oi_table, "VISAMPERR");
2930 for (cpl_size row = 0; row<cpl_table_get_nrow (oi_table); row++) {
2931 cpl_array_fill_window (array[row], 0, CPL_SIZE_MAX, err);
2932 }
2933 }
2934 }
2935
2936 /* VISPHIERR SC */
2937 err = gravi_param_get_double_default (parlist, "gravity.postprocess.visphierr-sc", -1.0);
2938 if ( err > 0) {
2939 cpl_msg_info (cpl_func,"Force VISPHIERR to %.e for all observations", err);
2940
2942 for (int pol = 0; pol < npol; pol++) {
2943 cpl_table * oi_table = gravi_data_get_oi_vis (oi_data, GRAVI_SC, pol, npol);
2944 cpl_array ** array = cpl_table_get_data_array (oi_table, "VISPHIERR");
2945 for (cpl_size row = 0; row<cpl_table_get_nrow (oi_table); row++) {
2946 cpl_array_fill_window (array[row], 0, CPL_SIZE_MAX, err);
2947 }
2948 }
2949 }
2950
2951 /* FLUXERR SC */
2952 err = gravi_param_get_double_default (parlist, "gravity.postprocess.fluxerr-sc", -1.0);
2953 if ( err > 0) {
2954 cpl_msg_info (cpl_func,"Force FLUXERR to %.e for all observations", err);
2955
2957 for (int pol = 0; pol < npol; pol++) {
2958 cpl_table * oi_table = gravi_data_get_oi_flux (oi_data, GRAVI_SC, pol, npol);
2959 cpl_array ** array = cpl_table_get_data_array (oi_table, "FLUXERR");
2960 for (cpl_size row = 0; row<cpl_table_get_nrow (oi_table); row++) {
2961 cpl_array_fill_window (array[row], 0, CPL_SIZE_MAX, err);
2962 }
2963 }
2964 }
2965
2966 /* VIS2ERR SC */
2967 err = gravi_param_get_double_default (parlist, "gravity.postprocess.vis2err-sc", -1.0);
2968 if ( err > 0) {
2969 cpl_msg_info (cpl_func,"Force VIS2ERR to %.e for all observations", err);
2970
2972 for (int pol = 0; pol < npol; pol++) {
2973 cpl_table * oi_table = gravi_data_get_oi_vis2 (oi_data, GRAVI_SC, pol, npol);
2974 cpl_array ** array = cpl_table_get_data_array (oi_table, "VIS2ERR");
2975 for (cpl_size row = 0; row<cpl_table_get_nrow (oi_table); row++) {
2976 cpl_array_fill_window (array[row], 0, CPL_SIZE_MAX, err);
2977 }
2978 }
2979 }
2980
2982 return CPL_ERROR_NONE;
2983}
2984
2985
2986/*----------------------------------------------------------------------------*/
2997/*----------------------------------------------------------------------------*/
2998
2999cpl_error_code gravi_average_vis (gravi_data * oi_data)
3000{
3002 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
3003
3004 gravi_msg_warning ("FIXME", "Average the different observation is EXPERIMENTAL");
3005
3006 cpl_msg_warning (cpl_func, "FIXME: Weightening of UVCOORD and MJD is not done properly yet !");
3007 cpl_msg_warning (cpl_func, "FIXME: Integration of INT_TIME is not done properly yet !");
3008
3009 int nbase = 6;
3010 cpl_table * oi_table;
3011
3012 /* Create output data */
3013 cpl_propertylist * header = gravi_data_get_header (oi_data);
3014
3015 /* Loop on oidata, type_data and polarisation */
3016 for (int type_data = 0; type_data < 2 ; type_data ++) {
3017
3018 if (!gravi_data_has_type (oi_data, type_data == GRAVI_SC ? "_SC" : "_FT")) {
3019 cpl_msg_info (cpl_func, "OI_VIS has no %s, skip", GRAVI_TYPE(type_data));
3020 continue;
3021 }
3022
3023 int npol = gravi_pfits_get_pola_num (header, type_data);
3024 for (int pol = 0 ; pol < npol ; pol++ ) {
3025
3026 cpl_size nrow = cpl_table_get_nrow (gravi_data_get_oi_vis (oi_data, type_data, pol, npol))/nbase;
3027 if (nrow == 1) {
3028 cpl_msg_info (cpl_func, "OI_VIS %s has only one observation, skip", GRAVI_TYPE(type_data));
3029 continue;
3030 }
3031
3032 /* OI_VIS */
3033 oi_table = gravi_data_get_oi_vis (oi_data, type_data, pol, npol);
3034 gravi_vis_average_value (oi_table, "TIME", NULL, 6);
3035 gravi_vis_average_value (oi_table, "MJD", NULL, 6);
3036 gravi_vis_average_value (oi_table, "INT_TIME", NULL, 6);
3037 gravi_vis_average_value (oi_table, "UCOORD", NULL, 6);
3038 gravi_vis_average_value (oi_table, "VCOORD", NULL, 6);
3039 gravi_vis_average_amp (oi_table, "VISAMP", "VISAMPERR", 6);
3040 gravi_vis_average_phi (oi_table, "VISPHI", "VISPHIERR", 6);
3041 gravi_vis_average_amp (oi_table, "RVIS", "RVISERR", 6);
3042 gravi_vis_average_amp (oi_table, "IVIS", "IVISERR", 6);
3043 // gravi_vis_average_amp (oi_table, "VISDATA", "VISERR"); // FIXME: to be done !!
3044 gravi_msg_warning ("FIXME", "VISDATA are not averaged !!!!");
3045 cpl_table_erase_window (oi_table, 6, CPL_SIZE_MAX);
3046
3047 CPLCHECK_MSG ("Cannot co-add OI_VIS");
3048
3049 /* OI_VIS2 */
3050 oi_table = gravi_data_get_oi_vis2 (oi_data, type_data, pol, npol);
3051 gravi_vis_average_value (oi_table, "TIME", NULL, 6);
3052 gravi_vis_average_value (oi_table, "MJD", NULL, 6);
3053 gravi_vis_average_value (oi_table, "INT_TIME", NULL, 6);
3054 gravi_vis_average_value (oi_table, "UCOORD", NULL, 6);
3055 gravi_vis_average_value (oi_table, "VCOORD", NULL, 6);
3056 gravi_vis_average_amp (oi_table, "VIS2DATA", "VIS2ERR", 6);
3057 cpl_table_erase_window (oi_table, 6, CPL_SIZE_MAX);
3058
3059 CPLCHECK_MSG ("Cannot co-add OI_VIS2");
3060
3061 /* OI_FLUX */
3062 oi_table = gravi_data_get_oi_flux (oi_data, type_data, pol, npol);
3063 gravi_vis_average_value (oi_table, "TIME", NULL, 4);
3064 gravi_vis_average_value (oi_table, "MJD", NULL, 4);
3065 gravi_vis_average_value (oi_table, "INT_TIME", NULL, 4);
3066 gravi_vis_average_amp (oi_table, "FLUX", "FLUXERR", 4);
3067 cpl_table_erase_window (oi_table, 4, CPL_SIZE_MAX);
3068
3069 CPLCHECK_MSG ("Cannot co-add OI_FLUX");
3070
3071 /* OI_T3 */
3072 oi_table = gravi_data_get_oi_t3 (oi_data, type_data, pol, npol);
3073 gravi_vis_average_value (oi_table, "TIME", NULL, 4);
3074 gravi_vis_average_value (oi_table, "MJD", NULL, 4);
3075 gravi_vis_average_value (oi_table, "INT_TIME", NULL, 4);
3076 gravi_vis_average_value (oi_table, "U1COORD", NULL, 4);
3077 gravi_vis_average_value (oi_table, "V1COORD", NULL, 4);
3078 gravi_vis_average_value (oi_table, "U2COORD", NULL, 4);
3079 gravi_vis_average_value (oi_table, "V2COORD", NULL, 4);
3080 gravi_vis_average_amp (oi_table, "T3AMP", "T3AMPERR", 4);
3081 gravi_vis_average_phi (oi_table, "T3PHI", "T3PHIERR", 4);
3082 cpl_table_erase_window (oi_table, 4, CPL_SIZE_MAX);
3083
3084 CPLCHECK_MSG ("Cannot co-add OI_T3");
3085
3086 } /* End loop on polarisation */
3087 } /* End loop on type_data */
3088
3090 return CPL_ERROR_NONE;
3091}
3092
3093/*----------------------------------------------------------------------------*/
3102/*----------------------------------------------------------------------------*/
3103
3104cpl_error_code gravi_vis_smooth_amp (cpl_table * oi_table, const char * name, const char * err,
3105 cpl_size nsamp)
3106{
3108 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3109 if (nsamp < 1) return CPL_ERROR_NONE;
3110 int nv;
3111
3112 /* Get values */
3113 cpl_size nwave = cpl_table_get_column_depth (oi_table, name);
3114 cpl_size nrow = cpl_table_get_nrow (oi_table);
3115 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3116
3117 /* Get arrays */
3118 cpl_array ** v_array = cpl_table_get_data_array (oi_table, name);
3119 cpl_array ** e_array = cpl_table_get_data_array (oi_table, err);
3120 cpl_array ** f_array = cpl_table_get_data_array (oi_table, "FLAG");
3121 CPLCHECK_MSG ("Cannot get data");
3122
3123 /* Allocate output */
3124 cpl_array * smo_array = cpl_array_duplicate (v_array[0]);
3125 cpl_array * err_array = cpl_array_duplicate (e_array[0]);
3126
3127 /* Loop on rows */
3128 for (cpl_size row = 0 ; row < nrow ; row ++) {
3129
3130 /* Median filter the uncertainties, to avoid
3131 * putting all on some sample */
3132 cpl_vector * i_vector = cpl_vector_new (nwave);
3133 for (cpl_size wave = 0; wave < nwave; wave++)
3134 cpl_vector_set (i_vector, wave, cpl_array_get (e_array[row],wave,&nv));
3135 cpl_vector * o_vector;
3136 o_vector = cpl_vector_filter_median_create (i_vector, nsamp);
3137
3138 /* Loop on waves */
3139 for (cpl_size wave = 0 ; wave < nwave ; wave ++) {
3140 double sum = 0.0, weight = 0.0;
3141
3142 /* Loop on samples to average */
3143 for (cpl_size samp = CPL_MAX(0,wave-nsamp) ; samp < CPL_MIN(nwave,wave+nsamp) ; samp ++) {
3144 if (cpl_array_get (f_array[row],samp,&nv)) {
3145 weight += 10e-20;
3146 sum += 0.0;
3147 } else {
3148 double w = pow (cpl_vector_get (o_vector,samp), -2);
3149 sum += cpl_array_get (v_array[row],samp,&nv) * w;
3150 weight += w;
3151 }
3152 }
3153
3154 cpl_array_set_double (smo_array, wave, sum / weight);
3155 cpl_array_set_double (err_array, wave, pow (weight, -0.5));
3156 }
3157
3158 /* Set back */
3159 cpl_table_set_array (oi_table, name, row, smo_array);
3160 cpl_table_set_array (oi_table, err, row, err_array);
3161 CPLCHECK_MSG ("Cannot smooth amp");
3162
3163 FREE (cpl_vector_delete, i_vector);
3164 FREE (cpl_vector_delete, o_vector);
3165 } /* End loop on rows */
3166
3167 FREE (cpl_array_delete, smo_array);
3168 FREE (cpl_array_delete, err_array);
3169
3171 return CPL_ERROR_NONE;
3172}
3173
3174/*----------------------------------------------------------------------------*/
3183/*----------------------------------------------------------------------------*/
3184
3185cpl_error_code gravi_vis_smooth_phi (cpl_table * oi_table, const char * name, const char * err,
3186 cpl_size nsamp)
3187{
3189 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3190 if (nsamp < 1) return CPL_ERROR_NONE;
3191
3192 /* Get values */
3193 cpl_size nwave = cpl_table_get_column_depth (oi_table, name);
3194 cpl_size nrow = cpl_table_get_nrow (oi_table);
3195 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3196 int nv;
3197
3198 /* Get arrays */
3199 cpl_array ** v_array = cpl_table_get_data_array (oi_table, name);
3200 cpl_array ** e_array = cpl_table_get_data_array (oi_table, err);
3201 cpl_array ** f_array = cpl_table_get_data_array (oi_table, "FLAG");
3202 CPLCHECK_MSG ("Cannot get data");
3203
3204 /* Allocate output */
3205 cpl_array * smo_array = cpl_array_duplicate (v_array[0]);
3206 cpl_array * err_array = cpl_array_duplicate (e_array[0]);
3207
3208 /* Loop on rows */
3209 for (cpl_size row = 0 ; row < nrow ; row ++) {
3210
3211 /* Median filter the uncertainties, to avoid
3212 * putting all on some sample */
3213 cpl_vector * i_vector = cpl_vector_new (nwave);
3214 for (cpl_size wave = 0; wave < nwave; wave++)
3215 cpl_vector_set (i_vector, wave, cpl_array_get (e_array[row],wave,&nv));
3216 cpl_vector * o_vector;
3217 o_vector = cpl_vector_filter_median_create (i_vector, nsamp);
3218
3219 /* Loop on waves */
3220 for (cpl_size wave = 0 ; wave < nwave ; wave ++) {
3221 double complex sum = 0.0 + I*0.0;
3222 double weight = 0.0;
3223
3224 /* Loop on samples to average */
3225 for (cpl_size samp = CPL_MAX(0,wave-nsamp) ; samp < CPL_MIN(nwave,wave+nsamp) ; samp ++) {
3226 if (cpl_array_get (f_array[row],samp,&nv)) {
3227 weight += 10e-20;
3228 sum += 0.0;
3229 } else {
3230 double w = pow (cpl_vector_get (o_vector,samp), -2);
3231 sum += cexp (1.*I* cpl_array_get (v_array[row],samp,&nv) * CPL_MATH_RAD_DEG) * w;
3232 weight += w;
3233 }
3234 }
3235
3236 cpl_array_set_double (smo_array, wave, carg (sum) * CPL_MATH_DEG_RAD);
3237 cpl_array_set_double (err_array, wave, pow (weight, -0.5));
3238 }
3239
3240 /* Set back */
3241 cpl_table_set_array (oi_table, name, row, smo_array);
3242 cpl_table_set_array (oi_table, err, row, err_array);
3243 CPLCHECK_MSG ("Cannot smooth phi");
3244
3245 FREE (cpl_vector_delete, i_vector);
3246 FREE (cpl_vector_delete, o_vector);
3247 } /* End loop on rows */
3248
3249 FREE (cpl_array_delete, smo_array);
3250 FREE (cpl_array_delete, err_array);
3251
3253 return CPL_ERROR_NONE;
3254}
3255
3256/*----------------------------------------------------------------------------*/
3265/*----------------------------------------------------------------------------*/
3266
3267cpl_error_code gravi_vis_fit_amp (cpl_table * oi_table, const char * name,
3268 const char * err, cpl_size maxdeg)
3269{
3271 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3272 if (maxdeg < 0) return CPL_ERROR_NONE;
3273
3274 /* Get values */
3275 cpl_size nwave = cpl_table_get_column_depth (oi_table, name);
3276 cpl_size nrow = cpl_table_get_nrow (oi_table);
3277 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3278 int nv;
3279
3280 /* Get arrays */
3281 cpl_array ** v_array = cpl_table_get_data_array (oi_table, name);
3282 cpl_array ** e_array = cpl_table_get_data_array (oi_table, err);
3283 cpl_array ** f_array = cpl_table_get_data_array (oi_table, "FLAG");
3284 CPLCHECK_MSG ("Cannot get data");
3285
3286 /* Loop on rows */
3287 for (cpl_size row = 0 ; row < nrow ; row ++) {
3288
3289 /* Create the vectors and matrix */
3290 cpl_matrix * coeff = cpl_matrix_new (nwave,maxdeg+1);
3291 cpl_matrix * rhs = cpl_matrix_new (nwave,1);
3292
3293 /* Fill */
3294 for (cpl_size wave = 0 ; wave < nwave ; wave ++) {
3295 double weight = cpl_array_get (f_array[row],wave,&nv) ? 10e-20 :
3296 pow (cpl_array_get (e_array[row],wave,&nv), -2);
3297 double value = cpl_array_get (f_array[row],wave,&nv) ? 0.0 :
3298 cpl_array_get (v_array[row],wave,&nv);
3299
3300 if (weight > 1e10)
3301 {
3302 cpl_msg_warning (cpl_func, "name = %s row = %lli wave = %lli "
3303 "has faulty uncertainty", name, row, wave);
3304 weight = 0.0;
3305 cpl_array_set (f_array[row],wave,1);
3306 }
3307
3308 cpl_matrix_set (rhs, wave, 0, value * weight);
3309 for (cpl_size deg = 0; deg <= maxdeg; deg++)
3310 cpl_matrix_set (coeff, wave, deg, pow ((double)wave,(double)deg) * weight);
3311 CPLCHECK_MSG ("Cannot fill");
3312 }
3313
3314 //printf ("name = %s row = %i maxdeg = %i\n", name, row, maxdeg);
3315 //cpl_matrix_dump (rhs, NULL);
3316 //cpl_matrix_dump (coeff, NULL);
3317
3318 /* Solve */
3319 cpl_errorstate prev_state = cpl_errorstate_get();
3320 cpl_matrix * solve = cpl_matrix_solve_normal (coeff, rhs);
3321
3322 /* Dump errors */
3323 if ( !cpl_errorstate_is_equal (prev_state))
3324 {
3325 cpl_errorstate_dump (prev_state, 0, NULL);
3326 cpl_msg_error (cpl_func,"%s row=%lld",name,row);
3327 }
3328 CPLCHECK_MSG ("Cannot solve matrix");
3329
3330 /* Evaluate */
3331 for (cpl_size wave = 0 ; wave < nwave ; wave ++) {
3332 double value = 0;
3333 for (cpl_size deg = 0; deg <= maxdeg; deg++)
3334 value += cpl_matrix_get (solve, deg, 0) * pow (wave, deg);
3335 cpl_array_set (v_array[row],wave,value);
3336 CPLCHECK_MSG ("Cannot evaluate");
3337 }
3338
3339 FREE (cpl_matrix_delete, coeff);
3340 FREE (cpl_matrix_delete, rhs);
3341 FREE (cpl_matrix_delete, solve);
3342 }
3343
3345 return CPL_ERROR_NONE;
3346}
3347
3348/*----------------------------------------------------------------------------*/
3362/*----------------------------------------------------------------------------*/
3363
3364cpl_error_code gravi_vis_smooth (gravi_data * oi_data,
3365 cpl_size nsamp_vis,
3366 cpl_size nsamp_flx,
3367 cpl_size maxdeg)
3368{
3370 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
3371
3372 cpl_table * oi_table;
3373
3374 /* Create output data */
3375 cpl_propertylist * header = gravi_data_get_header (oi_data);
3376
3377 int type_data = GRAVI_SC;
3378 int npol = gravi_pfits_get_pola_num (header, type_data);
3379
3380 for (int pol = 0 ; pol < npol ; pol++ ) {
3381
3382 /* OI_FLUX */
3383 oi_table = gravi_data_get_oi_flux (oi_data, type_data, pol, npol);
3384 gravi_vis_flag_nan (oi_table);
3385 gravi_vis_flag_lower (oi_table, "FLUXERR", "FLAG", 0.0);
3386 gravi_vis_smooth_amp (oi_table, "FLUX", "FLUXERR", nsamp_flx);
3387 gravi_vis_flag_relative_threshold (oi_table, "FLUXERR", "FLUX", "FLAG", 1.0);
3388 CPLCHECK_MSG ("Cannot resamp OI_FLUX");
3389
3390 /* OI_VIS2 */
3391 oi_table = gravi_data_get_oi_vis2 (oi_data, type_data, pol, npol);
3392 gravi_vis_flag_nan (oi_table);
3393 gravi_vis_flag_lower (oi_table, "VIS2ERR", "FLAG", 0.);
3394 gravi_vis_flag_median (oi_table, "VIS2ERR", "FLAG", 5.0);
3395 gravi_vis_smooth_amp (oi_table, "VIS2DATA", "VIS2ERR", nsamp_vis);
3396 gravi_vis_fit_amp (oi_table, "VIS2DATA", "VIS2ERR", maxdeg);
3397 gravi_vis_flag_threshold (oi_table, "VIS2ERR", "FLAG", 1.);
3398 CPLCHECK_MSG ("Cannot resamp OI_VIS2");
3399
3400 /* OI_VIS */
3401 oi_table = gravi_data_get_oi_vis (oi_data, type_data, pol, npol);
3402 gravi_vis_flag_nan (oi_table);
3403 gravi_vis_flag_lower (oi_table, "VISAMPERR", "FLAG", 0.);
3404 gravi_vis_flag_median (oi_table, "VISPHIERR", "FLAG", 5.0);
3405 gravi_vis_smooth_amp (oi_table, "VISAMP", "VISAMPERR", nsamp_vis);
3406 gravi_vis_smooth_phi (oi_table, "VISPHI", "VISPHIERR", nsamp_vis);
3407 gravi_vis_fit_amp (oi_table, "VISAMP", "VISAMPERR", maxdeg);
3408 gravi_vis_fit_amp (oi_table, "VISPHI", "VISPHIERR", maxdeg);
3409 gravi_vis_smooth_amp (oi_table, "RVIS", "RVISERR", nsamp_flx);
3410 gravi_vis_smooth_amp (oi_table, "IVIS", "IVISERR", nsamp_flx);
3411 gravi_vis_flag_threshold (oi_table, "VISAMPERR", "FLAG", 1.);
3412
3413 gravi_msg_warning ("FIXME", "VISDATA is not properly smooth !!");
3414 CPLCHECK_MSG ("Cannot resamp OI_VIS");
3415
3416 /* OI_T3 */
3417 oi_table = gravi_data_get_oi_t3 (oi_data, type_data, pol, npol);
3418 gravi_vis_flag_nan (oi_table);
3419 gravi_vis_flag_lower (oi_table, "T3AMPERR", "FLAG", 0.0);
3420 gravi_vis_flag_median (oi_table, "T3PHIERR", "FLAG", 5.0);
3421 gravi_vis_smooth_amp (oi_table, "T3AMP", "T3AMPERR", nsamp_vis);
3422 gravi_vis_smooth_phi (oi_table, "T3PHI", "T3PHIERR", nsamp_vis);
3423 gravi_vis_fit_amp (oi_table, "T3AMP", "T3AMPERR", maxdeg);
3424 gravi_vis_fit_amp (oi_table, "T3PHI", "T3PHIERR", maxdeg);
3425 gravi_vis_flag_threshold (oi_table, "T3AMPERR", "FLAG", 1.0);
3426 CPLCHECK_MSG ("Cannot resamp OI_T3");
3427
3428 } /* End loop on polarisation */
3429
3431 return CPL_ERROR_NONE;
3432}
3433
3434/*----------------------------------------------------------------------------*/
3444/*----------------------------------------------------------------------------*/
3445
3446cpl_error_code gravi_vis_resamp_amp (cpl_table * oi_table, const char * name, const char * err,
3447 cpl_size nsamp, cpl_size nwave_new)
3448{
3450 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3451
3452 /* Loop on rows */
3453 cpl_size nrow = cpl_table_get_nrow (oi_table);
3454 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3455 for (cpl_size row = 0 ; row < nrow ; row ++) {
3456
3457 /* Loop on new waves */
3458 for (cpl_size wave = 0 ; wave < nwave_new ; wave ++) {
3459 double sum = 0.0;
3460 double weight = 0.0;
3461 for (cpl_size samp = 0 ; samp < nsamp ; samp ++) {
3462 double w = pow (gravi_table_get_value (oi_table,err,row,wave*nsamp+samp), -2.0);
3463 if (gravi_table_get_value (oi_table,"FLAG",row,wave*nsamp+samp)) w = 10e-20;
3464 sum += gravi_table_get_value (oi_table,name,row,wave*nsamp+samp) * w;
3465 weight += w;
3466 }
3467 gravi_table_set_value (oi_table,name,row,wave, sum / weight);
3468 gravi_table_set_value (oi_table,err,row,wave, pow (weight, -0.5));
3469 }
3470
3471 } /* End loop on rows */
3472
3473 cpl_table_set_column_depth (oi_table, name, nwave_new);
3474 cpl_table_set_column_depth (oi_table, err, nwave_new);
3475
3477 return CPL_ERROR_NONE;
3478}
3479
3480/*----------------------------------------------------------------------------*/
3490/*----------------------------------------------------------------------------*/
3491
3492cpl_error_code gravi_vis_resamp_phi (cpl_table * oi_table, const char * name, const char * err,
3493 cpl_size nsamp, cpl_size nwave_new)
3494{
3496 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3497
3498 /* Loop on rows */
3499 cpl_size nrow = cpl_table_get_nrow (oi_table);
3500 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3501 for (cpl_size row = 0 ; row < nrow ; row ++) {
3502
3503 /* Loop on new waves */
3504 for (cpl_size wave = 0 ; wave < nwave_new ; wave ++) {
3505 double complex sum = 0.0;
3506 double weight = 0.0;
3507 for (cpl_size samp = 0 ; samp < nsamp ; samp ++) {
3508 double w = pow (gravi_table_get_value (oi_table,err,row,wave*nsamp+samp), -2.0);
3509 if (gravi_table_get_value (oi_table,"FLAG",row,wave*nsamp+samp)) w = 10e-20;
3510 sum += cexp (1.*I* gravi_table_get_value (oi_table,name,row,wave*nsamp+samp) * CPL_MATH_RAD_DEG) * w;
3511 weight += w;
3512 }
3513 gravi_table_set_value (oi_table,name,row,wave, carg (sum) * CPL_MATH_DEG_RAD);
3514 gravi_table_set_value (oi_table,err,row,wave, pow (weight, -0.5));
3515 }
3516
3517 } /* End loop on rows */
3518
3519 cpl_table_set_column_depth (oi_table, name, nwave_new);
3520 cpl_table_set_column_depth (oi_table, err, nwave_new);
3521
3523 return CPL_ERROR_NONE;
3524}
3525
3526/*----------------------------------------------------------------------------*/
3537/*----------------------------------------------------------------------------*/
3538
3539cpl_error_code gravi_vis_resamp (gravi_data * oi_data, cpl_size nsamp)
3540{
3542 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
3543 cpl_ensure_code (nsamp>1, CPL_ERROR_ILLEGAL_INPUT);
3544
3545 cpl_table * oi_table;
3546 cpl_size nwave, nwave_new;
3547 int nv = 0;
3548
3549 /* Create output data */
3550 cpl_propertylist * header = gravi_data_get_header (oi_data);
3551
3552 int type_data = GRAVI_SC;
3553 int npol = gravi_pfits_get_pola_num (header, type_data);
3554 for (int pol = 0 ; pol < npol ; pol++ ) {
3555
3556 /* OI_WAVELENGTH table */
3557 oi_table = gravi_data_get_oi_wave (oi_data, type_data, pol, npol);
3558 nwave = cpl_table_get_nrow (oi_table);
3559
3560 /* New number of wave sample */
3561 nwave_new = nwave / nsamp;
3562 cpl_msg_info (cpl_func, "Resamp the SC data by %lld bins: %lld -> %lld",
3563 nsamp, nwave, nwave_new);
3564 cpl_ensure_code (nwave_new > 1, CPL_ERROR_ILLEGAL_INPUT);
3565
3566 /* Get the wavelength */
3567 for (cpl_size wave = 0 ; wave < nwave_new ; wave ++) {
3568 /* Compute effective band first */
3569 cpl_table_set (oi_table, "EFF_BAND", wave,
3570 cpl_table_get (oi_table, "EFF_WAVE", wave*nsamp+nsamp-1, &nv) -
3571 cpl_table_get (oi_table, "EFF_WAVE", wave*nsamp, &nv));
3572
3573 /* Average them */
3574 double mean = 0.0;
3575 for (cpl_size samp = 0 ; samp < nsamp ; samp++)
3576 mean += cpl_table_get (oi_table, "EFF_WAVE", wave*nsamp+samp, &nv);
3577 cpl_table_set (oi_table, "EFF_WAVE", wave, mean / nsamp);
3578 }
3579
3580 /* Erase last entries */
3581 cpl_table_erase_window (oi_table, nwave_new, CPL_SIZE_MAX);
3582 CPLCHECK_MSG ("Cannot resamp OI_WAVELENGTH");
3583
3584 /* OI_FLUX */
3585 oi_table = gravi_data_get_oi_flux (oi_data, type_data, pol, npol);
3586 gravi_vis_resamp_amp (oi_table, "FLUX", "FLUXERR", nsamp, nwave_new);
3587 cpl_table_set_column_depth (oi_table, "FLAG", nwave_new);
3588 gravi_vis_flag_relative_threshold (oi_table, "FLUXERR", "FLUX", "FLAG", 1.0);
3589 CPLCHECK_MSG ("Cannot resamp OI_FLUX");
3590
3591 /* OI_VIS2 */
3592 oi_table = gravi_data_get_oi_vis2 (oi_data, type_data, pol, npol);
3593 gravi_vis_resamp_amp (oi_table, "VIS2DATA", "VIS2ERR", nsamp, nwave_new);
3594 cpl_table_set_column_depth (oi_table, "FLAG", nwave_new);
3595 gravi_vis_flag_threshold (oi_table, "VIS2ERR", "FLAG", 1.);
3596 CPLCHECK_MSG ("Cannot resamp OI_VIS2");
3597
3598 /* OI_VIS */
3599 oi_table = gravi_data_get_oi_vis (oi_data, type_data, pol, npol);
3600 gravi_vis_resamp_amp (oi_table, "VISAMP", "VISAMPERR", nsamp, nwave_new);
3601 gravi_vis_resamp_amp (oi_table, "VISPHI", "VISPHIERR", nsamp, nwave_new);
3602 gravi_vis_resamp_amp (oi_table, "RVIS", "RVISERR", nsamp, nwave_new);
3603 gravi_vis_resamp_amp (oi_table, "IVIS", "IVISERR", nsamp, nwave_new);
3604 cpl_table_set_column_depth (oi_table, "FLAG", nwave_new);
3605 gravi_vis_flag_threshold (oi_table, "VISAMPERR", "FLAG", 1.);
3606
3607 gravi_msg_warning ("FIXME", "VISDATA is not properly resampled !!");
3608 cpl_table_set_column_depth (oi_table, "VISDATA", nwave_new);
3609 cpl_table_set_column_depth (oi_table, "VISERR", nwave_new);
3610 CPLCHECK_MSG ("Cannot resamp OI_VIS");
3611
3612 /* OI_T3 */
3613 oi_table = gravi_data_get_oi_t3 (oi_data, type_data, pol, npol);
3614 gravi_vis_resamp_amp (oi_table, "T3AMP", "T3AMPERR", nsamp, nwave_new);
3615 gravi_vis_resamp_amp (oi_table, "T3PHI", "T3PHIERR", nsamp, nwave_new);
3616 cpl_table_set_column_depth (oi_table, "FLAG", nwave_new);
3617 gravi_vis_flag_threshold (oi_table, "T3AMPERR", "FLAG", 1.0);
3618 CPLCHECK_MSG ("Cannot resamp OI_T3");
3619
3620 } /* End loop on polarisation */
3621
3623 return CPL_ERROR_NONE;
3624}
3625
3626/*----------------------------------------------------------------------------*/
3634/*----------------------------------------------------------------------------*/
3635
3636cpl_error_code gravi_vis_copy_fluxdata (gravi_data * oi_data, int delete_flux)
3637{
3639 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
3640
3641 /* header */
3642 cpl_propertylist * header = gravi_data_get_header (oi_data);
3643
3644 /* Loop on oidata, type_data and polarisation */
3645 for (int type_data = 0; type_data < 2 ; type_data ++) {
3646
3647 if (!gravi_data_has_type (oi_data, type_data == GRAVI_SC ? "_SC" : "_FT")) {
3648 cpl_msg_info (cpl_func, "OI_FLUX has no %s, skip", GRAVI_TYPE(type_data));
3649 continue;
3650 }
3651
3652 int npol = gravi_pfits_get_pola_num (header, type_data);
3653 for (int pol = 0 ; pol < npol ; pol++ ) {
3654
3655 /* OI_FLUX table */
3656 cpl_table * oi_flux;
3657 oi_flux = gravi_data_get_oi_flux (oi_data, type_data, pol, npol);
3658
3659 /* Delete column if existing */
3660 if (cpl_table_has_column (oi_flux, "FLUXDATA") )
3661 cpl_table_erase_column (oi_flux, "FLUXDATA");
3662
3663 /* Duplicate FLUX into FLUXDATA */
3664 cpl_table_duplicate_column (oi_flux, "FLUXDATA", oi_flux, "FLUX");
3665
3666 /* Delete original FLUX column if so requested */
3667 if(delete_flux)
3668 cpl_table_erase_column(oi_flux, "FLUX");
3669 } /* End loop on polarisation */
3670
3671 } /* End loop on SC/FT */
3672
3674 return CPL_ERROR_NONE;
3675}
3676
3677/*----------------------------------------------------------------------------*/
3683/*----------------------------------------------------------------------------*/
3684
3685cpl_error_code gravi_vis_flag_nan (cpl_table * oi_table)
3686{
3688 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3689
3690 cpl_size nrow = cpl_table_get_nrow (oi_table);
3691 cpl_ensure_code (nrow > 0, CPL_ERROR_ILLEGAL_INPUT);
3692
3693 int ncols = 10;
3694 const char * names[] = {"VIS2DATA","VIS2ERR","VISAMP","VISAMPERR",
3695 "VISPHI","VISPHIERR","T3PHI","T3PHIERR",
3696 "T3AMP","T3AMPERR"};
3697
3698 /* Loop on columns */
3699 for (int c = 0; c < ncols; c++) {
3700
3701 if (!cpl_table_has_column (oi_table,names[c])) continue;
3702 cpl_msg_info (cpl_func,"Check column %s",names[c]);
3703
3704 /* Get data of this columns */
3705 cpl_size nwave = cpl_table_get_column_depth (oi_table, names[c]);
3706 cpl_array ** v_array = cpl_table_get_data_array (oi_table, names[c]);
3707 cpl_array ** f_array = cpl_table_get_data_array (oi_table, "FLAG");
3708 CPLCHECK_MSG ("Cannot get data");
3709
3710 /* Loop on rows and waves */
3711 cpl_size ninvalid = 0;
3712 for (cpl_size row = 0; row < nrow ; row ++) {
3713 for (cpl_size wave = 0 ; wave < nwave ; wave ++) {
3714
3715 /* Get value */
3716 int nv = 0;
3717 double value = cpl_array_get (v_array[row], wave, &nv);
3718
3719 /* Check value */
3720 if (nv || isnan (value)) {
3721 cpl_array_set (f_array[row], wave, 1.0);
3722 cpl_array_set (v_array[row], wave, 0.0);
3723 ninvalid ++;
3724 }
3725 CPLCHECK_MSG ("Cannot check data");
3726 }
3727 } /* End loop on rows and waves */
3728
3729 /* Verbose */
3730 if (ninvalid > 0) {
3731 cpl_msg_warning (cpl_func, "Flag %lld invalid data (NAN or NULL) in %s", ninvalid, names[c]);
3732 }
3733
3734 } /* End loop on columns */
3735
3737 return CPL_ERROR_NONE;
3738}
3739
3740/*----------------------------------------------------------------------------*/
3752/*----------------------------------------------------------------------------*/
3753
3754cpl_error_code gravi_vis_flag_threshold (cpl_table * oi_table, const char * data, const char *flag, double value)
3755{
3757 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3758 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
3759 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_OUTPUT);
3760
3761 /* Get pointer to speed up */
3762 int nv = 0;
3763 cpl_size nrow = cpl_table_get_nrow (oi_table);
3764 cpl_array ** pdata = cpl_table_get_data_array (oi_table, data);
3765 cpl_array ** pflag = cpl_table_get_data_array (oi_table, flag);
3766
3767 CPLCHECK_MSG ("Cannot get data");
3768
3769 cpl_size size = cpl_array_get_size (pdata[0]);
3770
3771 /* Loop on row and index. Add to FLAG if data is above threshold */
3772 for ( cpl_size row = 0 ; row < nrow ; row ++ ) {
3773 if (pdata[row]==NULL) continue;
3774
3775 for ( cpl_size indx = 0 ; indx < size ; indx ++ ) {
3776 if ( cpl_array_get (pdata[row], indx, &nv) > value ) {
3777 cpl_array_set (pflag[row], indx, cpl_array_get (pflag[row], indx, &nv) + 1 );
3778 }
3779 }
3780 }
3781
3783 return CPL_ERROR_NONE;
3784}
3785
3786/*----------------------------------------------------------------------------*/
3798/*----------------------------------------------------------------------------*/
3799
3800cpl_error_code gravi_vis_flag_lower (cpl_table * oi_table, const char * data, const char *flag, double value)
3801{
3803 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3804 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
3805 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_OUTPUT);
3806
3807 /* Get pointer to speed up */
3808 int nv = 0;
3809 cpl_size nrow = cpl_table_get_nrow (oi_table);
3810 cpl_array ** pdata = cpl_table_get_data_array (oi_table, data);
3811 cpl_array ** pflag = cpl_table_get_data_array (oi_table, flag);
3812
3813 CPLCHECK_MSG ("Cannot get data");
3814
3815 cpl_size size = cpl_array_get_size (pdata[0]);
3816
3817 /* Loop on row and index. Add to FLAG if data is above threshold */
3818 for ( cpl_size row = 0 ; row < nrow ; row ++ ) {
3819 if (pdata[row]==NULL) continue;
3820
3821 for ( cpl_size indx = 0 ; indx < size ; indx ++ ) {
3822 if ( cpl_array_get (pdata[row], indx, &nv) <= value ) {
3823 cpl_array_set (pflag[row], indx, cpl_array_get (pflag[row], indx, &nv) + 1 );
3824 }
3825 }
3826 }
3827
3829 return CPL_ERROR_NONE;
3830}
3831
3832/*----------------------------------------------------------------------------*/
3844/*----------------------------------------------------------------------------*/
3845
3846cpl_error_code gravi_vis_flag_median (cpl_table * oi_table, const char * data, const char *flag, double value)
3847{
3849 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3850 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
3851 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_OUTPUT);
3852
3853 /* Get pointer to speed up */
3854 int nv = 0;
3855 cpl_size nrow = cpl_table_get_nrow (oi_table);
3856 cpl_array ** pdata = cpl_table_get_data_array (oi_table, data);
3857 cpl_array ** pflag = cpl_table_get_data_array (oi_table, flag);
3858
3859 CPLCHECK_MSG ("Cannot get data");
3860
3861 cpl_size size = cpl_array_get_size (pdata[0]);
3862 cpl_vector * i_vector = cpl_vector_new (size);
3863
3864 /* Loop on row and index. Add to FLAG if data is above threshold */
3865 for ( cpl_size row = 0 ; row < nrow ; row ++ ) {
3866 if (pdata[row]==NULL || size<100) continue;
3867
3868 /* Set */
3869 for (cpl_size indx = 0; indx < size; indx++)
3870 cpl_vector_set (i_vector, indx, cpl_array_get (pdata[0],indx,&nv));
3871
3872 /* Median filter over 8 pixels wide */
3873 cpl_vector * o_vector = cpl_vector_filter_median_create (i_vector, 4);
3874
3875 /* Check whose pixel have a large values compare to this median */
3876 for ( cpl_size indx = 0 ; indx < size ; indx ++ ) {
3877 if ( cpl_array_get (pdata[row], indx, &nv) > value * cpl_vector_get (o_vector, indx)) {
3878 cpl_array_set (pflag[row], indx, cpl_array_get (pflag[row], indx, &nv) + 1 );
3879 }
3880 }
3881
3882 FREE (cpl_vector_delete, o_vector);
3883 }
3884
3885 FREE (cpl_vector_delete, i_vector);
3887 return CPL_ERROR_NONE;
3888}
3889
3890
3891/*----------------------------------------------------------------------------*/
3904/*----------------------------------------------------------------------------*/
3905
3906cpl_error_code gravi_vis_flag_relative_threshold(cpl_table * oi_table, const char * err,
3907 const char * data, const char *flag, double value)
3908{
3910 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3911 cpl_ensure_code (data, CPL_ERROR_NULL_INPUT);
3912 cpl_ensure_code (err, CPL_ERROR_NULL_INPUT);
3913 cpl_ensure_code (flag, CPL_ERROR_ILLEGAL_OUTPUT);
3914
3915 /* Get pointer to speed up */
3916 int nv = 0;
3917 cpl_size row, nrow = cpl_table_get_nrow (oi_table);
3918 cpl_array ** perr = cpl_table_get_data_array (oi_table, err);
3919 cpl_array ** pdata = cpl_table_get_data_array (oi_table, data);
3920 cpl_array ** pflag = cpl_table_get_data_array (oi_table, flag);
3921
3922 CPLCHECK_MSG ("Cannot get data");
3923
3924 cpl_size indx, size = cpl_array_get_size (pdata[0]);
3925
3926 /* Loop on row and index. Add to FLAG if data is above threshold */
3927 for ( row = 0 ; row < nrow ; row ++ ) {
3928 if (perr[row]==NULL) continue;
3929 cpl_array * tmp = cpl_array_duplicate (perr[row]);
3930 cpl_array_divide (tmp, pdata[row]);
3931 for ( indx = 0 ; indx < size ; indx ++ ) {
3932 if ( cpl_array_get (tmp, indx, &nv) > value) {
3933 cpl_array_set (pflag[row], indx, cpl_array_get (pflag[row], indx, &nv) + 1 );
3934 }
3935 }
3936 cpl_array_delete (tmp);
3937 }
3938
3940 return CPL_ERROR_NONE;
3941}
3942
3943/*----------------------------------------------------------------------------*/
3954/*----------------------------------------------------------------------------*/
3955
3956cpl_error_code gravi_vis_erase_obs (cpl_table * oi_table, cpl_array *flag_array, cpl_size ntel)
3957{
3959 cpl_ensure_code (oi_table, CPL_ERROR_NULL_INPUT);
3960 cpl_ensure_code (flag_array, CPL_ERROR_NULL_INPUT);
3961
3962 /* Get nrow */
3963 cpl_size nrow = cpl_table_get_nrow (oi_table) / ntel;
3964 cpl_ensure_code (nrow == cpl_array_get_size (flag_array),
3965 CPL_ERROR_ILLEGAL_INPUT);
3966
3967 /* Loop and select */
3968 cpl_table_unselect_all (oi_table);
3969 for (cpl_size row = 0; row < nrow; row++) {
3970 if (cpl_array_get (flag_array, row, NULL) == 0) continue;
3971 cpl_table_or_selected_window (oi_table, row * ntel, ntel);
3972 }
3973
3974 /* Delete selected */
3975 cpl_table_erase_selected (oi_table);
3976 CPLCHECK_MSG ("Cannot erase");
3977
3979 return CPL_ERROR_NONE;
3980}
3981
3982/*----------------------------------------------------------------------------*/
4002/*----------------------------------------------------------------------------*/
4003
4004cpl_error_code gravi_vis_compute_column_mean (cpl_table * out_table,
4005 cpl_table * in_table,
4006 const char * name, int ntel)
4007{
4009 cpl_ensure_code (out_table, CPL_ERROR_NULL_INPUT);
4010 cpl_ensure_code (in_table, CPL_ERROR_NULL_INPUT);
4011 cpl_ensure_code (name, CPL_ERROR_NULL_INPUT);
4012 cpl_ensure_code (ntel == cpl_table_get_nrow (out_table),
4013 CPL_ERROR_ILLEGAL_OUTPUT);
4014
4015 /* Check if column exist */
4016 if ( !cpl_table_has_column (in_table, name)) {
4017 cpl_msg_info (cpl_func, "Cannot average column %s (not existing)", name);
4018 return CPL_ERROR_NONE;
4019 }
4020
4021 /* Cast the type into an int, to avoid warnings */
4022 int type = cpl_table_get_column_type (in_table, name);
4023 cpl_size depth = cpl_table_get_column_depth (in_table, name);
4024
4025 /* Get the number of rows */
4026 cpl_size nrow = cpl_table_get_nrow (in_table) / ntel;
4027 cpl_ensure_code (nrow, CPL_ERROR_ILLEGAL_INPUT);
4028
4029 /* Get the column REJECTION_FLAG */
4030 int * flag = NULL;
4031 if (cpl_table_has_column (in_table, "REJECTION_FLAG"))
4032 flag = cpl_table_get_data_int (in_table, "REJECTION_FLAG");
4033
4034 cpl_msg_info (cpl_func, "Average column: %s (%s REJECTION_FLAG)",
4035 name, flag ? "with" : "without");
4036
4037 switch (type) {
4038 case CPL_TYPE_DOUBLE:
4039 case CPL_TYPE_FLOAT:
4040 case CPL_TYPE_INT:
4041 /* Case scalar column */
4042 if (!cpl_table_has_column (out_table, name))
4043 cpl_table_new_column (out_table, name, CPL_TYPE_DOUBLE);
4044 for (int tel = 0; tel < ntel; tel++) {
4045 cpl_size nvalid = 0;
4046 double mean = 0.0;
4047 for (cpl_size row = 0; row < nrow; row++) {
4048 if (flag && flag[row*ntel+tel] != 0) continue;
4049 nvalid ++;
4050 mean += cpl_table_get (in_table, name, row*ntel+tel, NULL);
4051 }
4052 if (nvalid > 0) mean /= nvalid;
4053 cpl_table_set (out_table, name, tel, mean);
4054 }
4055 break;
4056
4057 case CPL_TYPE_POINTER|CPL_TYPE_DOUBLE:
4058 case CPL_TYPE_POINTER|CPL_TYPE_FLOAT:
4059 case CPL_TYPE_POINTER|CPL_TYPE_INT:
4060 /* Case real array column */
4061 if (!cpl_table_has_column (out_table, name))
4062 cpl_table_new_column_array (out_table, name, CPL_TYPE_DOUBLE, depth);
4063 for (int tel = 0; tel < ntel; tel++) {
4064 cpl_size nvalid = 0;
4065 cpl_array * mean = gravi_array_init_double (depth, 0.0);
4066 for (cpl_size row = 0; row < nrow; row++) {
4067 if (flag && flag[row*ntel+tel] != 0) continue;
4068 nvalid ++;
4069 cpl_array_add (mean, cpl_table_get_array (in_table, name, row*ntel+tel));
4070 CPLCHECK_MSG ("Cannot add arrays...");
4071 }
4072 if (nvalid > 0) cpl_array_divide_scalar (mean, nvalid);
4073 cpl_table_set_array (out_table, name, tel, mean);
4074 FREE (cpl_array_delete, mean);
4075 }
4076 break;
4077
4078 case CPL_TYPE_POINTER|CPL_TYPE_DOUBLE_COMPLEX:
4079 case CPL_TYPE_POINTER|CPL_TYPE_FLOAT_COMPLEX:
4080 /* Case complex array column */
4081 if (!cpl_table_has_column (out_table, name))
4082 cpl_table_new_column_array (out_table, name, CPL_TYPE_DOUBLE_COMPLEX, depth);
4083 for (int tel = 0; tel < ntel; tel++) {
4084 cpl_size nvalid = 0;
4085 cpl_array * mean = gravi_array_init_double_complex (depth, 0.0*I+0.0);
4086 for (cpl_size row = 0; row < nrow; row++) {
4087 if (flag && flag[row*ntel+tel] != 0) continue;
4088 nvalid ++;
4089 cpl_array_add (mean, cpl_table_get_array (in_table, name, row*ntel+tel));
4090 }
4091 if (nvalid > 0) cpl_array_divide_scalar (mean, nvalid);
4092 cpl_table_set_array (out_table, name, tel, mean);
4093
4094 FREE (cpl_array_delete, mean);
4095 }
4096 break;
4097
4098 cpl_msg_error (cpl_func, "Type column not yet supported...");
4099 cpl_error_set_message (cpl_func, CPL_ERROR_ILLEGAL_INPUT,"This type is not supported.");
4100 return CPL_ERROR_ILLEGAL_INPUT;
4101 }
4102
4103 /* Copy units */
4104 cpl_table_set_column_unit (out_table, name, cpl_table_get_column_unit (in_table, name));
4105
4107 return CPL_ERROR_NONE;
4108}
4109
4110/*----------------------------------------------------------------------------*/
4122/*----------------------------------------------------------------------------*/
4123
4124cpl_error_code gravi_vis_force_time (gravi_data * oi_data)
4125{
4127 cpl_ensure_code (oi_data, CPL_ERROR_NULL_INPUT);
4128
4129 /* Number of extensions */
4130 cpl_size nb_ext = gravi_data_get_size (oi_data);
4131 cpl_ensure_code (nb_ext>0, CPL_ERROR_ILLEGAL_INPUT);
4132
4133 /* Init averaging */
4134 double mean_mjd = 0.0;
4135 double mean_time = 0.0;
4136 cpl_size count = 0;
4137
4138 /* Loop on extensions */
4139 for (int ext = 0; ext < nb_ext; ext++) {
4140
4141 /* Check if data table */
4142 const char * extname = gravi_data_get_extname (oi_data, ext);
4143 if (!strcmp (extname, "OI_VIS") || !strcmp (extname, "OI_VIS2") ||
4144 !strcmp (extname, "OI_T3") || !strcmp (extname, "OI_FLUX")) {
4145
4146 /* Average MJD and TIME */
4147 cpl_table * oi_table = gravi_data_get_table_x (oi_data, ext);
4148 mean_mjd += cpl_table_get_column_mean (oi_table, "MJD");
4149 mean_time += cpl_table_get_column_mean (oi_table, "TIME");
4150 count ++;
4151
4152 CPLCHECK_MSG ("Cannot get TIME or MJD...");
4153 }
4154 }
4155
4156 /* Compute mean */
4157 cpl_ensure_code (count>0, CPL_ERROR_ILLEGAL_INPUT);
4158 mean_mjd /= count;
4159 mean_time /= count;
4160
4161 /* Verbose */
4162 cpl_msg_info (cpl_func, "Mean MDJ = %g [mdj]", mean_mjd);
4163 cpl_msg_info (cpl_func, "Mean TIME = %g [s]", mean_time);
4164
4165 /* Loop on extensions */
4166 for (int ext = 0; ext < nb_ext; ext++) {
4167
4168 /* Check if data table */
4169 const char * extname = gravi_data_get_extname (oi_data, ext);
4170 if (!strcmp (extname, "OI_VIS") || !strcmp (extname, "OI_VIS2") ||
4171 !strcmp (extname, "OI_T3") || !strcmp (extname, "OI_FLUX")) {
4172
4173 /* Set MJD and TIME */
4174 cpl_table * oi_table = gravi_data_get_table_x (oi_data, ext);
4175 cpl_table_fill_column_window (oi_table, "MJD", 0, CPL_SIZE_MAX, mean_mjd);
4176 cpl_table_fill_column_window (oi_table, "TIME", 0, CPL_SIZE_MAX, mean_time);
4177
4178 CPLCHECK_MSG ("Cannot set average TIME or MJD...");
4179 }
4180 }
4181
4183 return CPL_ERROR_NONE;
4184}
4185
4186
#define gravi_table_set_value(table, name, row, value, val)
Definition: gravi_cpl.h:49
#define gravi_table_get_value(table, name, row, value)
Definition: gravi_cpl.h:48
typedefCPL_BEGIN_DECLS struct _gravi_data_ gravi_data
Definition: gravi_data.h:38
#define gravi_data_get_oi_t3(data, type, pol, npol)
Definition: gravi_data.h:47
#define gravi_data_get_oi_flux(data, type, pol, npol)
Definition: gravi_data.h:48
#define gravi_data_get_header(data)
Definition: gravi_data.h:74
#define gravi_data_get_oi_vis2(data, type, pol, npol)
Definition: gravi_data.h:46
#define gravi_data_get_oi_wave(data, type, pol, npol)
Definition: gravi_data.h:44
#define gravi_data_get_oi_vis_plist(data, type, pol, npol)
Definition: gravi_data.h:69
#define gravi_data_get_oi_vis(data, type, pol, npol)
Definition: gravi_data.h:45
#define gravi_data_get_extname(data, ext)
Definition: gravi_data.h:75
const cpl_size ntel
cpl_propertylist * gravi_idp_compute(gravi_data *vis_data, cpl_propertylist *header, cpl_frameset *frameset)
Create IDP keywords to satisfy standard.
Definition: gravi_idp.c:45
cpl_msg_debug(cpl_func, "Spectra has <50 pixels -> don't flat")
cpl_propertylist * header
Definition: gravi_old.c:2004
cpl_propertylist * plist
Definition: gravi_old.c:2000
cpl_msg_info(cpl_func, "Compute WAVE_SCAN for %s", GRAVI_TYPE(type_data))
cpl_propertylist_update_double(header, "ESO QC MINWAVE SC", cpl_propertylist_get_double(plist, "ESO QC MINWAVE SC"))
#define GRAVI_OI_VIS2_EXT
Definition: gravi_pfits.h:95
#define GRAVI_INSNAME(type, pol, npol)
Definition: gravi_pfits.h:198
#define GRAVI_OI_TARGET_EXT
Definition: gravi_pfits.h:86
#define GRAVI_OI_ARRAY_EXT
Definition: gravi_pfits.h:83
#define GRAVI_SC
Definition: gravi_pfits.h:165
#define GRAVI_OI_VIS_EXT
Definition: gravi_pfits.h:92
#define GRAVI_OI_FLUX_EXT
Definition: gravi_pfits.h:93
#define GRAVI_NIGHT_OBS
Definition: gravi_pfits.h:36
#define GRAVI_OI_T3_EXT
Definition: gravi_pfits.h:94
#define GRAVI_TYPE(type)
Definition: gravi_pfits.h:167
#define GRAVI_FT
Definition: gravi_pfits.h:166
#define GRAVI_OI_WAVELENGTH_EXT
Definition: gravi_pfits.h:91
#define gravi_msg_function_exit(flag)
Definition: gravi_utils.h:85
#define FREE(function, variable)
Definition: gravi_utils.h:69
#define CPLCHECK_NUL(msg)
Definition: gravi_utils.h:48
#define gravi_msg_function_start(flag)
Definition: gravi_utils.h:84
#define CPLCHECK_MSG(msg)
Definition: gravi_utils.h:45
#define gravi_pow2(data)
Definition: gravi_utils.h:81
#define FREELOOP(function, variable, n)
Definition: gravi_utils.h:72
cpl_error_code gravi_table_set_array_double_complex(cpl_table *table, const char *name, cpl_size row, cpl_array *visR, cpl_array *visI)
Definition: gravi_cpl.c:646
cpl_table * gravi_table_extract_time_interval(cpl_table *table, double start, double end)
Extract rows from table based on the TIME column.
Definition: gravi_cpl.c:3193
double gravi_table_get_column_mean(cpl_table *table, const char *name, int base, int nbase)
Definition: gravi_cpl.c:275
cpl_error_code gravi_table_new_column(cpl_table *table, const char *name, const char *unit, cpl_type type)
Definition: gravi_cpl.c:1588
cpl_error_code gravi_table_set_array_phase(cpl_table *table, const char *name, cpl_size row, cpl_array *phase)
Definition: gravi_cpl.c:670
cpl_array * gravi_array_init_double(long n, double value)
Definition: gravi_cpl.c:529
cpl_error_code gravi_array_get_group_delay_loop(cpl_array **input, cpl_array **flag, cpl_array *sigma, double *gd, cpl_size nrow, double max_width, int verbose)
Optimized computation of GDELAY for a list of arrays.
Definition: gravi_cpl.c:1335
cpl_array * gravi_table_get_column_sum_array(cpl_table *table, const char *name, int base, int nbase)
Definition: gravi_cpl.c:359
cpl_array * gravi_array_compute_norm2(cpl_array *input_re, cpl_array *input_im)
Definition: gravi_cpl.c:620
int gravi_array_threshold_min(cpl_array *array, double lo_cut)
Definition: gravi_cpl.c:71
cpl_array * gravi_array_rebin(const cpl_array *input, const cpl_array *errs, cpl_table *oi_wave_sc, cpl_table *oi_wave_ft)
Definition: gravi_cpl.c:724
cpl_array * gravi_array_init_double_complex(long n, double complex value)
Definition: gravi_cpl.c:551
cpl_array ** gravi_array_new_list(int n, cpl_type type, int size)
Allocate a list of arrays, pre-filled with 0.0.
Definition: gravi_cpl.c:93
cpl_error_code gravi_array_multiply_phasor(cpl_array *input, double complex factor, cpl_array *phase)
Multiply a REAL phase to a COMPLEX array, in-place: input = input * cexp (factor * phase)
Definition: gravi_cpl.c:1091
cpl_array * gravi_array_wrap_complex(cpl_array *input_re, cpl_array *input_im)
Definition: gravi_cpl.c:573
cpl_propertylist * gravi_data_get_extra_primary_header(gravi_data *self)
Get the propertylist for additional keywords to the primary header.
Definition: gravi_data.c:2074
gravi_data * gravi_data_new(int nb_ext)
Create an empty gravi_data.
Definition: gravi_data.c:110
cpl_error_code gravi_data_add_table(gravi_data *self, cpl_propertylist *plist, const char *extname, cpl_table *table)
Add a BINTABLE extension in gravi_data.
Definition: gravi_data.c:2289
int gravi_data_has_type(gravi_data *self, const char *type)
Return the number of ext whose EXTNAME and INSNAME match 'type'.
Definition: gravi_data.c:1833
cpl_table * gravi_data_get_table(gravi_data *self, const char *extname)
Return a pointer on a table extension by its EXTNAME.
Definition: gravi_data.c:2096
cpl_propertylist * gravi_data_get_plist_x(gravi_data *self, int i)
Get the propertylist of an extension by position.
Definition: gravi_data.c:1876
int gravi_data_get_size(const gravi_data *self)
Get the number of extension in a gravi_data.
Definition: gravi_data.c:828
cpl_error_code gravi_data_copy_ext(gravi_data *output, gravi_data *input, const char *name)
Copy extensions from one data to another.
Definition: gravi_data.c:1690
cpl_table * gravi_data_get_table_x(gravi_data *self, int i)
Get the table of an extension by position.
Definition: gravi_data.c:1901
int gravi_param_get_bool(const cpl_parameterlist *parlist, const char *name)
Definition: gravi_dfs.c:1537
const char * gravi_param_get_string(const cpl_parameterlist *parlist, const char *name)
Definition: gravi_dfs.c:1550
int gravi_param_get_int(const cpl_parameterlist *parlist, const char *name)
Definition: gravi_dfs.c:1524
double gravi_param_get_double(const cpl_parameterlist *parlist, const char *name)
Definition: gravi_dfs.c:1511
double gravi_param_get_double_default(const cpl_parameterlist *parlist, const char *name, double def)
Get the parameter from the parameter list.
Definition: gravi_dfs.c:1463
int gravi_pfits_get_pola_num(const cpl_propertylist *plist, int type_data)
Definition: gravi_pfits.c:263
const char * gravi_pfits_get_mode_name(const cpl_propertylist *plist)
Definition: gravi_pfits.c:242
double gravi_pfits_get_sobj_y(const cpl_propertylist *plist)
Definition: gravi_pfits.c:461
double gravi_pfits_get_metfc_lockmjd(const cpl_propertylist *plist, int tel)
Definition: gravi_pfits.c:295
double gravi_convert_to_mjd(const char *start)
Definition: gravi_pfits.c:1166
double gravi_pfits_get_dit_sc(const cpl_propertylist *plist)
Definition: gravi_pfits.c:664
double gravi_pfits_get_sobj_x(const cpl_propertylist *plist)
Definition: gravi_pfits.c:455
cpl_error_code gravi_apply_tf_amp(gravi_data *science, gravi_data *science_tf, gravi_data **used_tf_data, int num_tf_data, const char *extName, const char *insName, const char *ampName, const char *ampErrName, int nbase, double delta_t)
Interpolate the TF at the time of the science observation for an amplitude quantity.
Definition: gravi_tf.c:248
cpl_error_code gravi_msg_warning(const char *component, const char *msg)
Definition: gravi_utils.c:127
char GRAVI_BASE_NAME[6][3]
Definition: gravi_utils.c:57
int GRAVI_CLO_TEL[4][3]
Definition: gravi_utils.c:64
char GRAVI_CLO_NAME[4][4]
Definition: gravi_utils.c:65
cpl_table * gravi_table_oi_create(int nwave, int nrow, const char *oi_name)
Create the oi table (oi_vis, oi_vis2, oi_t3)
Definition: gravi_utils.c:153
int GRAVI_CLO_BASE[4][3]
Definition: gravi_utils.c:68
cpl_error_code gravi_vis_average_bootstrap(cpl_table *oi_vis_avg, cpl_table *oi_vis2_avg, cpl_table *oi_vis, int nboot, const char *phase_ref, int use_vFactor, int use_pFactor, int use_debiasing, double outlier_threshold)
Average the visibility of all DITs into a final, averaged value.
Definition: gravi_vis.c:915
cpl_error_code gravi_vis_resamp_amp(cpl_table *oi_table, const char *name, const char *err, cpl_size nsamp, cpl_size nwave_new)
Rebin amplitude column of OIFITS table.
Definition: gravi_vis.c:3446
cpl_error_code gravi_normalize_sc_to_ft(gravi_data *vis_data)
Align the SC visibilities on the FT visibilities.
Definition: gravi_vis.c:2565
cpl_error_code gravi_force_uncertainties(gravi_data *oi_data, const cpl_parameterlist *parlist)
Force uncertainties.
Definition: gravi_vis.c:2909
double gravi_randn(void)
Normal distribution pseudo-random generator.
Definition: gravi_vis.c:140
gravi_data * gravi_compute_vis(gravi_data *p2vmred_data, const cpl_parameterlist *parlist, cpl_size *current_frame)
The function average the individual frames of a P2VMREDUCED file into a final, single observation per...
Definition: gravi_vis.c:1676
cpl_error_code gravi_vis_fit_amp(cpl_table *oi_table, const char *name, const char *err, cpl_size maxdeg)
Smooth amp column of OIFITS table.
Definition: gravi_vis.c:3267
cpl_error_code gravi_flux_average_bootstrap(cpl_table *oi_flux_avg, cpl_table *oi_flux, int nboot, double outlier_threshold)
Average the flux of all DITs into a final, averaged value.
Definition: gravi_vis.c:274
cpl_error_code gravi_average_self_visphi(cpl_table *oi_vis_avg, cpl_table *oi_vis, cpl_array *wavenumber, const char *phase_ref, int *cmin, int *cmax, int nrange)
Compute Averaged VISPHI in the manner described, e.g., in F. Millour's thesis.
Definition: gravi_vis.c:1384
cpl_error_code gravi_vis_flag_nan(cpl_table *oi_table)
Flag samples of OIFITS table which are NAN or NULL.
Definition: gravi_vis.c:3685
cpl_error_code gravi_t3_average_bootstrap(cpl_table *oi_t3_avg, cpl_table *oi_vis, cpl_table *oi_flux, int nboot, int use_vFactor, int use_pFactor, double outlier_threshold)
Average the closure-phase of all DITs into a final, averaged value.
Definition: gravi_vis.c:510
cpl_error_code gravi_vis_smooth(gravi_data *oi_data, cpl_size nsamp_vis, cpl_size nsamp_flx, cpl_size maxdeg)
Smooth the SC table by nsamp consecutive spectral bins.
Definition: gravi_vis.c:3364
cpl_error_code gravi_vis_force_time(gravi_data *oi_data)
Force all data in OI_TABLE to have the same TIME and MJD.
Definition: gravi_vis.c:4124
cpl_error_code gravi_vis_mjd_to_time(gravi_data *vis_data)
Recompute the TIME column of all OIFITS extension from the MJD column, following the OIFITS standard ...
Definition: gravi_vis.c:2651
cpl_error_code gravi_vis_compute_column_mean(cpl_table *out_table, cpl_table *in_table, const char *name, int ntel)
Compute the mean of a column in OIFITS table, and save the result in the specified output table.
Definition: gravi_vis.c:4004
cpl_error_code gravi_vis_average_phi(cpl_table *oi_table, const char *name, const char *err, int nbase)
Average phases column of a multi-observation OIFITS table Phases are averaged with arg{<exp(i....
Definition: gravi_vis.c:2816
double gdAbacusErrPhi(double x)
Definition: gravi_vis.c:1315
cpl_error_code gravi_vis_smooth_phi(cpl_table *oi_table, const char *name, const char *err, cpl_size nsamp)
Smooth phase column of OIFITS table.
Definition: gravi_vis.c:3185
cpl_error_code gravi_vis_average_amp(cpl_table *oi_table, const char *name, const char *err, int nbase)
Average amplitudes column of a multi-observation OIFITS table The averaged quantities are stored in t...
Definition: gravi_vis.c:2755
cpl_error_code gravi_vis_copy_fluxdata(gravi_data *oi_data, int delete_flux)
Duplicate the column FLUX into FLUXDATA, for OIFITS2 compliance.
Definition: gravi_vis.c:3636
cpl_error_code gravi_vis_resamp(gravi_data *oi_data, cpl_size nsamp)
Re-bin the SC table by nsamp consecutive spectral bins.
Definition: gravi_vis.c:3539
cpl_error_code gravi_vis_resamp_phi(cpl_table *oi_table, const char *name, const char *err, cpl_size nsamp, cpl_size nwave_new)
Rebin phase column of OIFITS table (arg{<exp(i.phi)>})
Definition: gravi_vis.c:3492
cpl_error_code gravi_data_get_minmax_uvcoord(const cpl_table *oi_vis2, double *min_uvcoord, double *max_uvcoord)
Compute the minimum and maximum values of sqrt(ucoord**2 + vcoord**2)
Definition: gravi_vis.c:2510
cpl_error_code gravi_array_online_variance(cpl_array *data, cpl_array *mean, cpl_array *variance, int n)
Definition: gravi_vis.c:161
cpl_error_code gravi_flat_flux(gravi_data *vis_data, gravi_data *p2vm_map)
Divide the OI_FLUX by OI_FLUX from the P2VM (no checks, no time distance...)
Definition: gravi_vis.c:2705
cpl_error_code gravi_array_online_variance_res(cpl_array **data, int n, int rephase)
On-line variance of arrays.
Definition: gravi_vis.c:221
cpl_error_code gravi_vis_flag_threshold(cpl_table *oi_table, const char *data, const char *flag, double value)
Flag samples of OIFITS table based on absolute threshold.
Definition: gravi_vis.c:3754
cpl_error_code gravi_vis_flag_relative_threshold(cpl_table *oi_table, const char *err, const char *data, const char *flag, double value)
Flag samples of OIFITS table based on relative threshold.
Definition: gravi_vis.c:3906
cpl_error_code gravi_vis_flag_lower(cpl_table *oi_table, const char *data, const char *flag, double value)
Flag samples of OIFITS table based on absolute threshold.
Definition: gravi_vis.c:3800
cpl_error_code gravi_average_vis(gravi_data *oi_data)
Coadd the observations together.
Definition: gravi_vis.c:2999
cpl_error_code gravi_vis_flag_median(cpl_table *oi_table, const char *data, const char *flag, double value)
Flag samples of OIFITS table based on runnning median.
Definition: gravi_vis.c:3846
cpl_error_code gravi_compute_vis_qc(gravi_data *vis_data, cpl_frameset *frameset)
The function compute the QC parameters for a VIS (averaged) data.
Definition: gravi_vis.c:2235
cpl_error_code gravi_vis_smooth_amp(cpl_table *oi_table, const char *name, const char *err, cpl_size nsamp)
Smooth amplitude column of OIFITS table.
Definition: gravi_vis.c:3104
cpl_error_code gravi_vis_average_value(cpl_table *oi_table, const char *name, const char *err, int nbase)
Average scalar column of a multi-observation OIFITS table. The averaged quantities are stored in the ...
Definition: gravi_vis.c:2872
cpl_error_code gravi_vis_erase_obs(cpl_table *oi_table, cpl_array *flag_array, cpl_size ntel)
Erase observation from an OIFITS table.
Definition: gravi_vis.c:3956