File: uves_reduce_utils.c

package info (click to toggle)
cpl-plugin-uves 6.1.3+dfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 23,128 kB
  • sloc: ansic: 171,056; sh: 4,359; python: 3,002; makefile: 1,322
file content (371 lines) | stat: -rw-r--r-- 13,755 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
/*                                                                              *
 *   This file is part of the ESO UVES Pipeline                                 *
 *   Copyright (C) 2004,2005 European Southern Observatory                      *
 *                                                                              *
 *   This library is free software; you can redistribute it and/or modify       *
 *   it under the terms of the GNU General Public License as published by       *
 *   the Free Software Foundation; either version 2 of the License, or          *
 *   (at your option) any later version.                                        *
 *                                                                              *
 *   This program is distributed in the hope that it will be useful,            *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of             *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
 *   GNU General Public License for more details.                               *
 *                                                                              *
 *   You should have received a copy of the GNU General Public License          *
 *   along with this program; if not, write to the Free Software                *
 *   Foundation, 51 Franklin St, Fifth Floor, Boston, MA  02111-1307  USA       *
 *                                                                              */

/*
 * $Author: amodigli $
 * $Date: 2013-10-11 12:43:10 $
 * $Revision: 1.17 $
 * $Name: not supported by cvs2svn $
 * $Log: not supported by cvs2svn $
 * Revision 1.15  2012/03/02 16:49:48  amodigli
 * fixed warning related to upgrade to CPL6
 *
 * Revision 1.14  2011/12/08 14:05:48  amodigli
 * Fix warnings with CPL6
 *
 * Revision 1.13  2010/09/24 09:32:07  amodigli
 * put back QFITS dependency to fix problem spot by NRI on FIBER mode (with MIDAS calibs) data
 *
 * Revision 1.11  2007/06/06 08:17:33  amodigli
 * replace tab with 4 spaces
 *
 * Revision 1.10  2007/04/24 12:50:29  jmlarsen
 * Replaced cpl_propertylist -> uves_propertylist which is much faster
 *
 * Revision 1.9  2007/04/10 07:09:37  jmlarsen
 * Changed interface of uves_spline_hermite()
 *
 * Revision 1.8  2006/11/06 15:19:41  jmlarsen
 * Removed unused include directives
 *
 * Revision 1.7  2006/08/17 13:56:53  jmlarsen
 * Reduced max line length
 *
 * Revision 1.6  2006/05/12 15:10:07  jmlarsen
 * Shortened lines
 *
 * Revision 1.5  2006/04/10 12:38:13  jmlarsen
 * Bugfix: don't read uninitialized memory (caused atmospheric extinction step 
 * to be randomly disabled)
 *
 * Revision 1.4  2006/04/06 08:49:23  jmlarsen
 * Propagate errors when normalizing spectrum
 *
 * Revision 1.3  2005/12/19 16:17:56  jmlarsen
 * Replaced bool -> int
 *
 * Revision 1.2  2005/12/16 14:22:23  jmlarsen
 * Removed midas test data; Added sof files
 *
 * Revision 1.1  2005/11/11 13:18:54  jmlarsen
 * Reorganized code, renamed source files
 *
 */

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

/*----------------------------------------------------------------------------*/
/**
 * @addtogroup uves_reduce
 */
/*----------------------------------------------------------------------------*/
/**@{*/

/*-----------------------------------------------------------------------------
                                Includes
 -----------------------------------------------------------------------------*/

#include <uves_reduce_utils.h>
#include <math.h>
#include <uves_pfits.h>
#include <uves_utils.h>
#include <uves_utils_wrappers.h>
#include <uves_error.h>
#include <uves_msg.h>

#include <cpl.h>

/*-----------------------------------------------------------------------------
                            Functions prototypes
 -----------------------------------------------------------------------------*/

/*-----------------------------------------------------------------------------
                            Implementation
 -----------------------------------------------------------------------------*/
static double
uves_get_airmass(const double z) {
    /* http://en.wikipedia.org/wiki/Air_mass_%28astronomy%29 */

      /* X= sec z * ( 1-0.0012( (sec z)^2 -1 ) ) */
    double x=z/180.*CPL_MATH_PI;

    double sec=1./cos(x);
    return ( sec * ( 1.-0.0012 * ( sec*sec-1. ) ) );

    /* Yung 1994
    double A= 1.002432*cos(x)*cos(x)+0.148386*cos(z)+0.0096467;
    double B= cos(x)*cos(x)*cos(x)+0.149864*cos(x)*cos(x)+0.0102963*cos(x)+0.000303978;
    return A/B;
    */


}

/*----------------------------------------------------------------------------*/
/**
   @brief    Normalize a spectrum
   @param    spectrum           The 1d (merged) or 2d (non-merged or 2d
                                extracted+merged) spectrum to be normalized
   @param    spectrum_error     Error (1 sigma) of @em spectrum, or NULL.
   @param    spectrum_header    Header describing the geometry of the input spectrum
   @param    raw_header         Header of the raw frame
   @param    n_traces           Number of spatial bins (1 unless 2d extracted)
   @param    chip               CCD chip
   @param    atm_extinction     The table of extinction coefficients
   @param    correct_binning    Flag indicating whether or not to divide by
                                the x-binning factor
   @param    scaled_error       (output) If non-NULL, error of output spectrum
   @return   The normalized spectrum

   The spectrum is divided by exposure time, gain and (optionally) binning. 
   Also corrected for atmospheric extinction using the provided table of
   extinction coefficients.

   Bad pixels are propagated.
*/
/*----------------------------------------------------------------------------*/
cpl_image *
uves_normalize_spectrum(const cpl_image *spectrum, const cpl_image *spectrum_error,
            const uves_propertylist *spectrum_header,
            const uves_propertylist *raw_header,
            int n_traces,
            enum uves_chip chip,
            const cpl_table *atm_extinction,
            bool correct_binning,
            cpl_image **scaled_error)
{
    cpl_image *scaled = NULL;
    double exptime, gain;
    int binx;
    int norders, ny, nx;
    
    assure_nomsg( spectrum != NULL, CPL_ERROR_NULL_INPUT);
    assure_nomsg( scaled_error == NULL || spectrum_error != NULL, CPL_ERROR_NULL_INPUT);
    assure_nomsg( spectrum_header != NULL, CPL_ERROR_NULL_INPUT);

    nx = cpl_image_get_size_x(spectrum);
    ny = cpl_image_get_size_y(spectrum);

    if (spectrum_error != NULL)
    {
        assure( nx == cpl_image_get_size_x(spectrum_error) &&
            ny == cpl_image_get_size_y(spectrum_error), CPL_ERROR_INCOMPATIBLE_INPUT,
            "Error spectrum geometry differs from spectrum: %" CPL_SIZE_FORMAT "x%" CPL_SIZE_FORMAT " vs. %d x %d",
            cpl_image_get_size_x(spectrum_error),
            cpl_image_get_size_y(spectrum_error),
            nx, ny);
    }
    
    assure( ny % n_traces == 0, CPL_ERROR_INCOMPATIBLE_INPUT,
        "Spectrum image height (%d) is not a multiple of "
        "the number of traces (%d). Confused, bailing out",
        ny, n_traces);
    
    norders = ny / n_traces;

    /*
     * Correct for exposure time, gain, bin 
     */
    check( exptime = uves_pfits_get_exptime(raw_header),
           "Could not read exposure time");
    
    check( gain = uves_pfits_get_gain(raw_header, chip),
       "Could not read gain factor");
    
    if (correct_binning)
    {
        /* x-binning of rotated image is y-binning of raw image */
        check( binx  = uves_pfits_get_biny(raw_header),
           "Could not read binning");
    }
    else
    {
        uves_msg("Spectrum will not be normalized to unit binning");
        binx = 1;
    }
    
    assure( exptime > 0, CPL_ERROR_ILLEGAL_INPUT, "Non-positive exposure time: %f s", exptime);
    assure( gain    > 0, CPL_ERROR_ILLEGAL_INPUT, "Non-positive gain: %f", gain);
    assure( binx    > 0, CPL_ERROR_ILLEGAL_INPUT, "Illegal binning: %d", binx);
    
    uves_msg("Correcting for exposure time = %f s, gain = %f, binx = %d", exptime, gain, binx);
    
    check( scaled        = cpl_image_divide_scalar_create(spectrum, exptime * gain * binx),
       "Error correcting spectrum for gain, exposure time, binning");
    
    if (scaled_error != NULL)
    {
        check( *scaled_error = cpl_image_divide_scalar_create(spectrum_error, 
                                  exptime * gain * binx),
           "Error correcting rebinned spectrum for gain, exposure time, binning");
    }
    
    /* 
     * Correct for atmospheric extinction 
     */
    {
    double airmass;
    double dlambda, lambda_start;
    int order;
    int miss_airm_start=0;
    int miss_airm_end=0;
    {
        double airmass_start, airmass_end;
        if(uves_propertylist_has(raw_header,UVES_AIRMASS_START)) {
            check( airmass_start = uves_pfits_get_airmass_start(raw_header),
                            "Error reading airmass start");
        } else {
            double alt = uves_pfits_get_tel_alt_start(raw_header);
            double z=90.-alt;
            miss_airm_start=1;

            airmass_start=uves_get_airmass(z);
            uves_msg_warning("Missing %s approximate it", UVES_AIRMASS_START);

        }
        if(uves_propertylist_has(raw_header,UVES_AIRMASS_END)) {
            check( airmass_end = uves_pfits_get_airmass_end(raw_header),
                            "Error reading airmass end");
        } else {
            double alt = uves_pfits_get_tel_alt_start(raw_header);
            double z=90.-alt;
            miss_airm_end=1;
            airmass_end=uves_get_airmass(z);
            uves_msg_warning("Missing %s approximate it", UVES_AIRMASS_END);

        }
        if(miss_airm_start && miss_airm_end) {
            uves_msg_error("Both airmass start and end aere missing. Stop");
            cpl_error_set(cpl_func,CPL_ERROR_ILLEGAL_INPUT);
        }  else {
            /* Use arithmetic mean of airmass start/end */
            airmass = (airmass_start + airmass_end) / 2;
        }

    }

    uves_msg("Correcting for extinction through airmass %f", airmass);
        
    check( dlambda = uves_pfits_get_cdelt1(spectrum_header),
           "Error reading bin width from header");
    
    for (order = 1; order <= norders; order++)
        {
        int trace;

        /* If spectrum was already merged, then read crval1,
         * otherwise read wstart for each order
         */
        
        if (norders == 1)
            {
            check( lambda_start = uves_pfits_get_crval1(spectrum_header),
                   "Error reading start wavelength from header");    
            }
        else
            {
            check( lambda_start = uves_pfits_get_wstart(spectrum_header, order),
                   "Error reading start wavelength from header");    
            }

        for (trace = 1; trace <= n_traces; trace++)
            {
            int spectrum_row = (order - 1)*n_traces + trace;
            int x;
            
            for (x = 1; x <= nx; x++)
                {
                int pis_rejected1;
                int pis_rejected2;
                double flux;
                double dflux = 0;
                double extinction;
                double lambda;

                lambda = lambda_start + (x-1) * dlambda;
                
                flux  = cpl_image_get(scaled, x, spectrum_row, &pis_rejected1);
                if (scaled_error != NULL)
                    {
                    dflux = cpl_image_get(*scaled_error, x, 
                                  spectrum_row, &pis_rejected2);
                    }

                if (!pis_rejected1 && (scaled_error == NULL || !pis_rejected2))
                    {
                                        int istart = 0;

                    /* Read extinction (units: magnitude per airmass) */
                    check( extinction = 
                           uves_spline_hermite_table(
                           lambda, atm_extinction,
                           "LAMBDA", "LA_SILLA", &istart),
                           "Error interpolating extinction coefficient");
                    
                    /* Correct for extinction using
                     * the magnitude/flux relation
                     * m = -2.5 log_10 F
                     *  => 
                     * F = 10^(-m*0.4)
                     *
                     * m_top-of-atmosphere = m - ext.coeff*airmass
                     * F_top-of-atmosphere = F * 10^(0.4 * ext.coeff*airmass)
                     */

                    cpl_image_set(
                        scaled, x, spectrum_row,
                        flux * pow(10, 0.4 * extinction * airmass));
                    if (scaled_error != NULL)
                        {
                        cpl_image_set(
                            *scaled_error, x, spectrum_row,
                            dflux * pow(10, 0.4 * extinction * airmass));
                        }
                    }
                else
                    {
                    cpl_image_reject(scaled, x, spectrum_row);
                    if (scaled_error != NULL)
                        {
                        cpl_image_reject(*scaled_error, x, spectrum_row);
                        }
                    }
                } /* for each x */

            } /* for each (possibly only 1) trace */

        } /* for each (possibly only 1) order */
    }
    
  cleanup:
    if (cpl_error_get_code() != CPL_ERROR_NONE)
    {
        uves_free_image(&scaled);
        if (scaled_error != NULL)
        {
            uves_free_image(scaled_error);
        }
    }
    
    return scaled;
}

/**@}*/