IIINSTRUMENT Pipeline Reference Manual  4.4.10
naco_spc_lampflat.c
1 /* $Id: naco_spc_lampflat.c,v 1.21 2011-12-22 11:21:03 llundin Exp $
2  *
3  * This file is part of the NACO 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., 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA
19  */
20 
21 /*
22  * $Author: llundin $
23  * $Date: 2011-12-22 11:21:03 $
24  * $Revision: 1.21 $
25  * $Name: not supported by cvs2svn $
26  */
27 
28 #ifdef HAVE_CONFIG_H
29 #include <config.h>
30 #endif
31 
32 /*-----------------------------------------------------------------------------
33  Includes
34  -----------------------------------------------------------------------------*/
35 
36 #include "naco_recipe.h"
37 
38 #include "naco_spc.h"
39 
40 /*-----------------------------------------------------------------------------
41  Recipe defines
42  -----------------------------------------------------------------------------*/
43 
44 #define RECIPE_STRING "naco_spc_lampflat"
45 
46 #ifndef NACO_SPC_MEDIAN_XSIZE
47 #define NACO_SPC_MEDIAN_XSIZE 200
48 #endif
49 
50 #ifndef NACO_SPC_MEDIAN_YSIZE
51 #define NACO_SPC_MEDIAN_YSIZE NACO_SPC_MEDIAN_XSIZE
52 #endif
53 
54 /*-----------------------------------------------------------------------------
55  Private Functions prototypes
56  -----------------------------------------------------------------------------*/
57 
58 static cpl_image * naco_spc_lampflat_reduce(cpl_propertylist *,
59  const irplib_framelist *,
60  const cpl_parameterlist *);
61 
62 static cpl_error_code naco_spc_lampflat_qc(cpl_propertylist *,
63  cpl_propertylist *,
64  const irplib_framelist *);
65 
66 static cpl_error_code naco_spc_lampflat_save(cpl_frameset *,
67  const cpl_parameterlist *,
68  const cpl_propertylist *,
69  const cpl_propertylist *,
70  const cpl_image *,
71  int, const irplib_framelist *);
72 
73 NACO_RECIPE_DEFINE(naco_spc_lampflat,
74  NACO_PARAM_REJBORD | NACO_PARAM_HOT_LIM | NACO_PARAM_COLD_LIM,
75  "Spectrocopic flat recipe using a lamp",
76  RECIPE_STRING " -- NACO spectrocopy flat-field creation from "
77  "lamp images.\n"
78  "The files listed in the Set Of Frames (sof-file) "
79  "must be tagged:\n"
80  "NACO-raw-file.fits " NACO_SPC_LAMPFLAT_RAW "\n"
81  "\n"
82  NACO_SPC_MAN_MODESPLIT "\n\n"
83  "Furthermore, the input set of frames must have values of "
84  "the FITS key "
85  NACO_PFITS_INT_LAMP2 " that of zero for off-frames and "
86  "non-zero for on-frames.\n");
87 
88 
89 /*----------------------------------------------------------------------------*/
93 /*----------------------------------------------------------------------------*/
94 
95 /*-----------------------------------------------------------------------------
96  Functions code
97  -----------------------------------------------------------------------------*/
98 
99 /*----------------------------------------------------------------------------*/
106 /*----------------------------------------------------------------------------*/
107 static int naco_spc_lampflat(cpl_frameset * framelist,
108  const cpl_parameterlist * parlist)
109 {
110  cpl_errorstate cleanstate = cpl_errorstate_get();
111  irplib_framelist * allframes = NULL;
112  irplib_framelist * rawframes = NULL;
113  irplib_framelist * f_one = NULL;
114  const char ** taglist = NULL;
115  cpl_image * lamp_flat = NULL;
116  cpl_propertylist * qclist = cpl_propertylist_new();
117  cpl_propertylist * paflist = cpl_propertylist_new();
118  int nb_good = 0;
119  int nsets;
120  int i;
121 
122 
123  /* Identify the RAW and CALIB frames in the input frameset */
124  skip_if (naco_dfs_set_groups(framelist));
125 
126  allframes = irplib_framelist_cast(framelist);
127  skip_if(allframes == NULL);
128 
129  rawframes = irplib_framelist_extract(allframes, NACO_SPC_LAMPFLAT_RAW);
130  skip_if(rawframes == NULL);
131  irplib_framelist_empty(allframes);
132 
133  skip_if(irplib_framelist_load_propertylist_all(rawframes, 0, "^("
134  NACO_PFITS_REGEXP_SPCFLAT "|"
135  NACO_PFITS_REGEXP_SPCFLAT_PAF
136  ")$", CPL_FALSE));
137 
138  taglist = naco_framelist_set_tag(rawframes, naco_spc_make_tag, &nsets);
139  skip_if(taglist == NULL);
140 
141  cpl_msg_info(cpl_func, "Identified %d setting(s) in %d frames",
142  nsets, irplib_framelist_get_size(rawframes));
143 
144  /* Extract settings and reduce each of them */
145  for (i=0 ; i < nsets ; i++) {
146 
147  /* Reduce data set nb i */
148  cpl_msg_info(cpl_func, "Reducing data set %d of %d", i+1, nsets);
149 
150  /* Reduce data set nb i */
151  f_one = irplib_framelist_extract(rawframes, taglist[i]);
152 
153  /* Reset the tag */
154  skip_if(irplib_framelist_set_tag_all(f_one, NACO_SPC_LAMPFLAT_RAW));
155 
156  cpl_msg_info(cpl_func, "Reducing frame set %d of %d (size=%d) with "
157  "setting: %s", i+1, nsets,
158  irplib_framelist_get_size(f_one), taglist[i]);
159 
160  skip_if (f_one == NULL);
161 
162  lamp_flat = naco_spc_lampflat_reduce(qclist, f_one, parlist);
163 
164  /* Save the products */
165  if (lamp_flat == NULL) {
166  if (nsets > 1)
167  irplib_error_recover(cleanstate, "Could not compute the flat for "
168  "this setting");
169  } else {
170  skip_if(naco_spc_lampflat_qc(qclist, paflist, f_one));
171  /* PRO.CATG */
172  bug_if (cpl_propertylist_append_string(paflist, CPL_DFS_PRO_CATG,
173  NACO_CALIB_SPCFLAT));
174  skip_if(naco_spc_lampflat_save(framelist, parlist, qclist, paflist,
175  lamp_flat, i+1, f_one));
176  cpl_image_delete(lamp_flat);
177  lamp_flat = NULL;
178  nb_good++;
179  }
180  cpl_propertylist_empty(qclist);
181  cpl_propertylist_empty(paflist);
182  irplib_framelist_delete(f_one);
183  f_one = NULL;
184  }
185 
186  irplib_ensure(nb_good > 0, CPL_ERROR_DATA_NOT_FOUND,
187  "None of the %d sets could be reduced", nsets);
188 
189  end_skip;
190 
191  cpl_free(taglist);
192  cpl_image_delete(lamp_flat);
193  irplib_framelist_delete(f_one);
194  irplib_framelist_delete(allframes);
195  irplib_framelist_delete(rawframes);
196  cpl_propertylist_delete(qclist);
197  cpl_propertylist_delete(paflist);
198 
199  return cpl_error_get_code();
200 }
201 
202 /*----------------------------------------------------------------------------*/
210 /*----------------------------------------------------------------------------*/
211 static cpl_image * naco_spc_lampflat_reduce(cpl_propertylist * qclist,
212  const irplib_framelist * framelist,
213  const cpl_parameterlist * parlist)
214 {
215  cpl_image * self = NULL;
216  cpl_imagelist * difflist = cpl_imagelist_new();
217  cpl_mask * bpm = NULL;
218  cpl_vector * medians = NULL;
219  const double hot_thresh
220  = naco_parameterlist_get_double(parlist, RECIPE_STRING,
221  NACO_PARAM_HOT_LIM);
222  const double cold_thresh = 1.0 /
223  naco_parameterlist_get_double(parlist, RECIPE_STRING,
224  NACO_PARAM_COLD_LIM);
225  const char * rej_bord
226  = naco_parameterlist_get_string(parlist, RECIPE_STRING,
227  NACO_PARAM_REJBORD);
228  cpl_propertylist * lampkeys = cpl_propertylist_new();
229  int rej_left, rej_right, rej_bottom, rej_top;
230  int nflat, nbad;
231  int ndiff, idiff;
232 
233 
234  skip_if (0);
235  bug_if (qclist == NULL);
236  bug_if (framelist == NULL);
237  bug_if (parlist == NULL);
238 
239  skip_if(cold_thresh <= 0.0);
240  skip_if(cold_thresh >= 1.0);
241  skip_if(hot_thresh <= 1.0);
242 
243  skip_if_ne(sscanf(rej_bord, "%d %d %d %d",
244  &rej_left, &rej_right, &rej_bottom, &rej_top), 4,
245  "number(s) in string parameter (%s): \"%s\"",
246  CPL_XSTRINGIFY(NACO_PARAM_REJBORD), rej_bord);
247 
248  /* On-frames have lamp2 on and lamp1 off */
249  bug_if(cpl_propertylist_append_int(lampkeys, NACO_PFITS_INT_LAMP2, 1));
250  bug_if(cpl_propertylist_append_int(lampkeys, NACO_PFITS_BOOL_LAMP1, 0));
251 
252  skip_if(naco_imagelist_load_diff(difflist, framelist, lampkeys));
253 
254  ndiff = cpl_imagelist_get_size(difflist);
255 
256  medians = cpl_vector_new(ndiff);
257 
258  bug_if(0);
259 
260  for (idiff = 0, nflat = 0; idiff < ndiff; idiff++) {
261  cpl_image * diff = cpl_imagelist_get(difflist, nflat);
262  const int nx = cpl_image_get_size_x(diff);
263  const int ny = cpl_image_get_size_y(diff);
264 
265  double median;
266  const double mean
267  = cpl_image_get_mean_window(diff,
268  rej_left, nx - rej_right,
269  rej_bottom, ny - rej_top);
270 
271  skip_if(0);
272 
273  if (mean <= 0.0) {
274  cpl_msg_warning(cpl_func, "Ignoring difference image %d with an "
275  "invalid mean: %g", 1+idiff, mean);
276  cpl_image_delete(cpl_imagelist_unset(difflist, nflat));
277  continue;
278  }
279 
280  /* Get the median of the central region */
281  median = cpl_image_get_median_window(diff,
282  (nx-NACO_SPC_MEDIAN_XSIZE)/2,
283  (ny-NACO_SPC_MEDIAN_YSIZE)/2,
284  (nx+NACO_SPC_MEDIAN_XSIZE)/2,
285  (ny+NACO_SPC_MEDIAN_YSIZE)/2);
286  skip_if(0);
287 
288  /* Normalize the difference image */
289  bug_if(cpl_image_divide_scalar(diff, mean));
290 
291  /* Find non-hot/cold pixels */
292  bpm = cpl_mask_threshold_image_create(diff, cold_thresh, hot_thresh);
293  bug_if(bpm == NULL);
294 
295  if (cpl_mask_is_empty(bpm)) {
296  cpl_msg_warning(cpl_func, "Ignoring difference image %d with no "
297  "good pixels", 1+idiff);
298  cpl_mask_delete(bpm);
299  bpm = NULL;
300  cpl_image_delete(cpl_imagelist_unset(difflist, nflat));
301  continue;
302  }
303 
304  bug_if(cpl_mask_not(bpm));
305 
306  cpl_msg_info(cpl_func, "Difference image %d has %d bad pixels", 1+idiff,
307  (int)cpl_mask_count(bpm));
308 
309  /* Reject hot and cold pixels */
310  bug_if(cpl_mask_or(cpl_image_get_bpm(diff), bpm));
311 
312  cpl_mask_delete(bpm);
313  bpm = NULL;
314 
315  bug_if (cpl_vector_set(medians, nflat, median));
316 
317  nflat++;
318  }
319 
320  bug_if(nflat != cpl_imagelist_get_size(difflist));
321 
322  error_if(nflat == 0, CPL_ERROR_DATA_NOT_FOUND,
323  "The %d difference images are all invalid", ndiff);
324 
325  self = cpl_imagelist_collapse_create(difflist);
326  bug_if(0);
327 
328  nbad = cpl_image_count_rejected(self);
329  bug_if(0);
330 
331  if (nbad > 0) {
332  cpl_msg_info(cpl_func, "Setting %d bad pixels in master flat to 1.0",
333  nbad);
334  bug_if(cpl_image_fill_rejected(self, 1.0));
335  }
336 
337  bug_if(cpl_vector_set_size(medians, nflat));
338 
339  bug_if(cpl_propertylist_append_double(qclist, "ESO QC SPECFLAT NCOUNTS",
340  cpl_vector_get_mean(medians)));
341  bug_if(cpl_propertylist_append_double(qclist, "ESO QC SPECFLAT STDEV",
342  cpl_vector_get_stdev(medians)));
343 
344  end_skip;
345 
346  if (cpl_error_get_code()) {
347  cpl_image_delete(self);
348  self = NULL;
349  }
350 
351  cpl_propertylist_delete(lampkeys);
352  cpl_imagelist_delete(difflist);
353  cpl_mask_delete(bpm);
354  cpl_vector_delete(medians);
355 
356  return self;
357 }
358 
359 
360 /*----------------------------------------------------------------------------*/
368 /*----------------------------------------------------------------------------*/
369 static cpl_error_code naco_spc_lampflat_qc(cpl_propertylist * qclist,
370  cpl_propertylist * paflist,
371  const irplib_framelist * rawframes)
372 {
373 
374  const cpl_propertylist * reflist
375  = irplib_framelist_get_propertylist_const(rawframes, 0);
376  const char pafcopy[] = "^(" NACO_PFITS_REGEXP_SPCFLAT_PAF ")$";
377 
378 
379  bug_if (0);
380 
381 
382  /* THE PAF FILE FOR QC PARAMETERS */
383  skip_if (cpl_propertylist_copy_property_regexp(paflist, reflist, pafcopy,
384  0));
385  skip_if (cpl_propertylist_append(paflist, qclist));
386 
387  bug_if (cpl_propertylist_copy_property_regexp(qclist, reflist, "^("
388  IRPLIB_PFITS_REGEXP_RECAL_LAMP
389  ")$", 0));
390 
391  end_skip;
392 
393  return cpl_error_get_code();
394 }
395 
396 /*----------------------------------------------------------------------------*/
408 /*----------------------------------------------------------------------------*/
409 static cpl_error_code naco_spc_lampflat_save(cpl_frameset * set_tot,
410  const cpl_parameterlist * parlist,
411  const cpl_propertylist * qclist,
412  const cpl_propertylist * paflist,
413  const cpl_image * flat,
414  int set_nb,
415  const irplib_framelist * rawframes)
416 {
417  cpl_frameset * proframes = irplib_frameset_cast(rawframes);
418  char * filename = NULL;
419 
420 
421 
422  /* This will catch rawframes == NULL */
423  bug_if (0);
424 
425  /* SAVE THE COMBINED IMAGE */
426  filename = cpl_sprintf(RECIPE_STRING "_set%02d" CPL_DFS_FITS, set_nb);
427  skip_if (irplib_dfs_save_image(set_tot, parlist, proframes, flat,
428  CPL_BPP_IEEE_FLOAT, RECIPE_STRING,
429  NACO_CALIB_SPCFLAT, qclist, NULL,
430  naco_pipe_id, filename));
431 
432 #ifdef NACO_SAVE_PAF
433  cpl_free(filename);
434  filename = cpl_sprintf(RECIPE_STRING "_set%02d" CPL_DFS_PAF, set_nb);
435  skip_if (cpl_dfs_save_paf("NACO", RECIPE_STRING, paflist, filename));
436 #else
437  bug_if(paflist == NULL);
438 #endif
439 
440  end_skip;
441 
442  cpl_free(filename);
443  cpl_frameset_delete(proframes);
444 
445  return cpl_error_get_code();
446 
447 }
naco_framelist_set_tag
const char ** naco_framelist_set_tag(irplib_framelist *self, char *(*pftag)(const cpl_frame *, const cpl_propertylist *, int), int *pntags)
Retag a framelist according to the given tagging function.
Definition: naco_utils.c:176
naco_spc_make_tag
char * naco_spc_make_tag(const cpl_frame *self, const cpl_propertylist *plist, int dummy)
Create a string suitable for frame comparison in spectroscopy.
Definition: naco_spc.c:407
naco_parameterlist_get_double
double naco_parameterlist_get_double(const cpl_parameterlist *self, const char *recipe, naco_parameter bitmask)
Retrieve the value of a NACO parameter of type double.
Definition: naco_parameter.c:538
naco_parameterlist_get_string
const char * naco_parameterlist_get_string(const cpl_parameterlist *self, const char *recipe, naco_parameter bitmask)
Retrieve the value of a NACO string parameter.
Definition: naco_parameter.c:604
naco_imagelist_load_diff
cpl_error_code naco_imagelist_load_diff(cpl_imagelist *self, const irplib_framelist *onofflist, const cpl_propertylist *onoffkeys)
Fill the list of difference images from on/off frames.
Definition: naco_spc.c:482
naco_dfs_set_groups
int naco_dfs_set_groups(cpl_frameset *set)
Set the group as RAW or CALIB in a frameset.
Definition: naco_dfs.c:62