uves_merge.c

00001 /*                                                                              *
00002  *   This file is part of the ESO UVES Pipeline                                 *
00003  *   Copyright (C) 2004,2005 European Southern Observatory                      *
00004  *                                                                              *
00005  *   This library is free software; you can redistribute it and/or modify       *
00006  *   it under the terms of the GNU General Public License as published by       *
00007  *   the Free Software Foundation; either version 2 of the License, or          *
00008  *   (at your option) any later version.                                        *
00009  *                                                                              *
00010  *   This program is distributed in the hope that it will be useful,            *
00011  *   but WITHOUT ANY WARRANTY; without even the implied warranty of             *
00012  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the              *
00013  *   GNU General Public License for more details.                               *
00014  *                                                                              *
00015  *   You should have received a copy of the GNU General Public License          *
00016  *   along with this program; if not, write to the Free Software                *
00017  *   Foundation, 51 Franklin St, Fifth Floor, Boston, MA  02111-1307  USA       *
00018  *                                                                              */
00019 
00020 
00021 /*
00022  * $Author: amodigli $
00023  * $Date: 2010/12/16 16:57:40 $
00024  * $Revision: 1.60 $
00025  * $Name: uves-4_9_1 $
00026  * $Log: uves_merge.c,v $
00027  * Revision 1.60  2010/12/16 16:57:40  amodigli
00028  * fixed compiler warnings
00029  *
00030  * Revision 1.59  2010/12/08 11:07:59  amodigli
00031  * added chip parameter to uves_merge_orders() to have proper filenames. Fixed content err data for noappend case
00032  *
00033  * Revision 1.58  2010/09/27 06:32:22  amodigli
00034  * fixed mem leaks
00035  *
00036  * Revision 1.57  2010/09/24 09:32:04  amodigli
00037  * put back QFITS dependency to fix problem spot by NRI on FIBER mode (with MIDAS calibs) data
00038  *
00039  * Revision 1.55  2010/06/07 09:48:00  amodigli
00040  * changed units: A-->Ang, FLUX-->ADU
00041  *
00042  * Revision 1.54  2010/06/01 16:06:55  amodigli
00043  * added unit [A] to reduced product
00044  *
00045  * Revision 1.53  2008/09/29 06:57:41  amodigli
00046  * add #include <string.h>
00047  *
00048  * Revision 1.52  2008/09/27 16:05:12  amodigli
00049  * fixed bug using delta parmeters
00050  *
00051  * Revision 1.51  2008/09/23 11:32:39  amodigli
00052  * added check on array upper bound access to fix DFS05803
00053  *
00054  * Revision 1.50  2008/08/29 09:52:39  amodigli
00055  * fixed compiler warning
00056  *
00057  * Revision 1.49  2008/06/26 08:30:38  amodigli
00058  * fixed bug in setting delta
00059  *
00060  * Revision 1.48  2008/06/11 14:42:50  amodigli
00061  * fixed seg fault
00062  *
00063  * Revision 1.45  2008/03/04 07:35:31  amodigli
00064  * generate spectra of each order only if NOAPPEND
00065  *
00066  * Revision 1.44  2008/02/21 07:50:38  amodigli
00067  * added method NOAPPEND
00068  *
00069  * Revision 1.43  2007/08/21 13:08:26  jmlarsen
00070  * Removed irplib_access module, largely deprecated by CPL-4
00071  *
00072  * Revision 1.42  2007/06/21 11:28:57  jmlarsen
00073  * Added support for type float (for FLAMES)
00074  *
00075  * Revision 1.41  2007/06/06 08:17:33  amodigli
00076  * replace tab with 4 spaces
00077  *
00078  * Revision 1.40  2007/05/03 15:21:13  jmlarsen
00079  * Decreased output message verbosity
00080  *
00081  * Revision 1.39  2007/04/24 12:50:29  jmlarsen
00082  * Replaced cpl_propertylist -> uves_propertylist which is much faster
00083  *
00084  * Revision 1.38  2007/02/09 08:57:54  jmlarsen
00085  * Include <float.h>
00086  *
00087  * Revision 1.37  2007/02/09 08:14:16  jmlarsen
00088  * Do not use CPL_PIXEL_MAXVAL which works only for integer images
00089  *
00090  * Revision 1.36  2007/02/08 07:34:28  jmlarsen
00091  * Minor doc change
00092  *
00093  * Revision 1.35  2006/11/15 15:02:14  jmlarsen
00094  * Implemented const safe workarounds for CPL functions
00095  *
00096  * Revision 1.33  2006/11/15 14:04:08  jmlarsen
00097  * Removed non-const version of parameterlist_get_first/last/next which is already
00098  * in CPL, added const-safe wrapper, unwrapper and deallocator functions
00099  *
00100  * Revision 1.32  2006/11/13 14:23:55  jmlarsen
00101  * Removed workarounds for CPL const bugs
00102  *
00103  * Revision 1.31  2006/11/06 15:19:41  jmlarsen
00104  * Removed unused include directives
00105  *
00106  * Revision 1.30  2006/09/11 14:00:11  jmlarsen
00107  * Minor documentation change
00108  *
00109  * Revision 1.29  2006/08/17 13:56:53  jmlarsen
00110  * Reduced max line length
00111  *
00112  * Revision 1.28  2006/08/17 09:16:47  jmlarsen
00113  * Removed CPL2 code
00114  *
00115  * Revision 1.27  2006/08/11 14:37:59  jmlarsen
00116  * Added input validation
00117  *
00118  * Revision 1.26  2006/08/10 10:50:12  jmlarsen
00119  * Removed workaround for cpl_image_get_bpm
00120  *
00121  * Revision 1.25  2006/07/03 13:16:42  jmlarsen
00122  * Reduced number of significant digits in message
00123  *
00124  * Revision 1.24  2006/04/06 08:38:56  jmlarsen
00125  * Changed char* -> const char* for static string
00126  *
00127  * Revision 1.23  2006/03/03 13:54:11  jmlarsen
00128  * Changed syntax of check macro
00129  *
00130  * Revision 1.22  2006/02/03 07:46:30  jmlarsen
00131  * Moved recipe implementations to ./uves directory
00132  *
00133  * Revision 1.21  2006/01/31 08:24:29  jmlarsen
00134  * Wrapper for cpl_image_get_bpm
00135  *
00136  * Revision 1.20  2006/01/25 16:13:20  jmlarsen
00137  * Changed interface of gauss.fitting routine
00138  *
00139  * Revision 1.19  2005/12/19 16:17:56  jmlarsen
00140  * Replaced bool -> int
00141  *
00142  * Revision 1.18  2005/12/16 14:22:23  jmlarsen
00143  * Removed midas test data; Added sof files
00144  *
00145  * Revision 1.17  2005/11/24 15:09:06  jmlarsen
00146  * Implemented 2d extraction/rebinning/merging
00147  *
00148  * Revision 1.16  2005/11/24 11:54:46  jmlarsen
00149  * Added support for CPL 3 interface
00150  *
00151  * Revision 1.15  2005/11/18 10:52:06  jmlarsen
00152  * Split into optimal/sum merge methods
00153  *
00154  * Revision 1.14  2005/11/11 13:18:54  jmlarsen
00155  * Reorganized code, renamed source files
00156  *
00157  */
00158 
00159 #ifdef HAVE_CONFIG_H
00160 #  include <config.h>
00161 #endif
00162 
00163 /*----------------------------------------------------------------------------*/
00169 /*----------------------------------------------------------------------------*/
00173 /*-----------------------------------------------------------------------------
00174                                 Includes
00175  -----------------------------------------------------------------------------*/
00176 
00177 #include <uves_merge.h>
00178 
00179 #include <uves_pfits.h>
00180 #include <uves_utils.h>
00181 #include <uves_utils_wrappers.h>
00182 #include <uves_dump.h>
00183 #include <uves_dfs.h>
00184 #include <uves_error.h>
00185 
00186 #include <cpl.h>
00187 #include <float.h>
00188 #include <string.h>
00189 /*-----------------------------------------------------------------------------
00190                             Functions prototypes
00191  ----------------------------------------------------------------------------*/
00192 
00193 /*-----------------------------------------------------------------------------
00194                             Implementation
00195  ----------------------------------------------------------------------------*/
00196 
00197 /*---------------------------------------------------------------------------*/
00224 /*---------------------------------------------------------------------------*/
00225 
00226 cpl_image *
00227 uves_merge_orders(const cpl_image *spectrum, 
00228                   const cpl_image *spectrum_noise,
00229                   const uves_propertylist *spectrum_header,
00230                   merge_method m_method,
00231                   int n_traces,
00232                   uves_propertylist **merged_header,
00233                   const double delt1, 
00234                   const double delt2,
00235                   enum uves_chip chip,
00236                   cpl_image **merged_noise)
00237 {
00238     cpl_image *merged = NULL;    /* Result */
00239 
00240     const double *spectrum_data_double = NULL;
00241     const float  *spectrum_data_float  = NULL;
00242     const cpl_mask *spectrum_badmap    = NULL;
00243     const cpl_binary *spectrum_bad     = NULL;
00244 
00245     const double *noise_data_double = NULL;
00246     const float *noise_data_float   = NULL;
00247     const cpl_mask *noise_badmap    = NULL;
00248     const cpl_binary *noise_bad     = NULL;
00249     cpl_type type;               /* input/output images type */
00250 
00251     int nbins, ny, norders;          /* Input image size. ny = norders*n_traces */
00252     double wavestep;
00253     int bin_min = 0, bin_max = 0;    /* wavelength of min/max bin in units of 'wavestep' */
00254     int total_bins;
00255     int order, trace;
00256     int spectrum_sx=0;
00257     int spectrum_sy=0;
00258     double delt1_bin=0;
00259     double delt2_bin=0;
00260     char* filename=NULL;
00261 
00262     cpl_vector* image_1d=NULL;
00263     uves_propertylist* hext=NULL;
00264     //double med_noise=0;
00265     passure( spectrum != NULL, " ");
00266     passure( spectrum_noise != NULL, " ");
00267     passure( spectrum_header != NULL, " ");
00268     passure( merged_header != NULL, " ");
00269     passure( merged_noise != NULL, " ");
00270 
00271     assure( m_method == MERGE_OPTIMAL || 
00272             m_method == MERGE_SUM || 
00273             m_method == MERGE_NOAPPEND, 
00274             CPL_ERROR_ILLEGAL_INPUT,
00275             "Unknown merge method: %d", m_method);
00276     
00277     assure( cpl_image_get_type(spectrum) == CPL_TYPE_DOUBLE ||
00278             cpl_image_get_type(spectrum) == CPL_TYPE_FLOAT,
00279             CPL_ERROR_TYPE_MISMATCH,
00280             "Spectrum must have type double or float. It is '%s'",
00281             uves_tostring_cpl_type(cpl_image_get_type(spectrum)));
00282     
00283     assure( cpl_image_get_type(spectrum_noise) == CPL_TYPE_DOUBLE ||
00284             cpl_image_get_type(spectrum_noise) == CPL_TYPE_FLOAT,
00285             CPL_ERROR_TYPE_MISMATCH,
00286             "Spectrum noise must have type double. It is '%s'",
00287             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)));
00288 
00289     assure( cpl_image_get_type(spectrum) ==
00290             cpl_image_get_type(spectrum_noise),
00291             CPL_ERROR_TYPE_MISMATCH,
00292             "Spectrum and spectrum noise must have same type. They are "
00293             "%s and %s, respectively",
00294             uves_tostring_cpl_type(cpl_image_get_type(spectrum)),
00295             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)) );
00296 
00297     type = cpl_image_get_type(spectrum);
00298 
00299     /* Read input spectrum geometry */
00300     nbins           = cpl_image_get_size_x(spectrum);
00301     ny              = cpl_image_get_size_y(spectrum);
00302 
00303     assure( cpl_image_get_size_x(spectrum_noise) == nbins &&
00304             cpl_image_get_size_y(spectrum_noise) == ny,
00305             CPL_ERROR_INCOMPATIBLE_INPUT,
00306             "Incompatible spectrum/noise image sizes: %dx%d vs. %dx%d",
00307             nbins, ny,
00308             cpl_image_get_size_x(spectrum_noise),
00309             cpl_image_get_size_y(spectrum_noise) );
00310     
00311     assure( ny % n_traces == 0, CPL_ERROR_INCOMPATIBLE_INPUT,
00312             "Spectrum image height (%d) is not a multiple of "
00313             "the number of traces (%d). Confused, bailing out",
00314             ny, n_traces);
00315 
00316     norders         = ny / n_traces;
00317     
00318     check( wavestep = uves_pfits_get_cdelt1(spectrum_header),
00319        "Error reading bin width");
00320 
00321     /* Get data pointers (for efficiency) */
00322    
00323     if (type == CPL_TYPE_DOUBLE) {
00324         spectrum_data_double   = cpl_image_get_data_double_const(spectrum);
00325     }
00326     else {
00327         spectrum_data_float   = cpl_image_get_data_float_const(spectrum);
00328     }
00329 
00330     spectrum_sx=cpl_image_get_size_x(spectrum);
00331     spectrum_sy=cpl_image_get_size_y(spectrum);
00332 
00333     spectrum_badmap = cpl_image_get_bpm_const(spectrum);
00334     spectrum_bad    = cpl_mask_get_data_const(spectrum_badmap);
00335     
00336     if (type == CPL_TYPE_DOUBLE) {
00337         noise_data_double = cpl_image_get_data_double_const(spectrum_noise);        
00338     }
00339     else {
00340         noise_data_float  = cpl_image_get_data_float_const(spectrum_noise);
00341     }
00342     noise_badmap = cpl_image_get_bpm_const(spectrum_noise);
00343     noise_bad    = cpl_mask_get_data_const(noise_badmap);
00344     uves_msg("delt1=%f delt2=%f",delt1,delt2);
00345     /* Read max/min lambda */
00346     for (order = 1; order <= norders; order++)
00347     {
00348         double wstart, wend;
00349         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00350            "Error reading start wavelength for order #%d", order);
00351 
00352         check( wend = uves_pfits_get_wend(spectrum_header, order),
00353            "Error reading end wavelength for order #%d", order);
00354         
00355         uves_msg_debug("Order #%d: wstart - wend = %f - %f wlu", order, wstart, wend);
00356 
00357     //wstart+=delt1;
00358     //wend-=delt2;
00359 
00360         if (order == 1)
00361         {
00362             bin_min = uves_round_double(wstart/wavestep);
00363             bin_max = uves_round_double(wend  /wavestep);
00364         }
00365         
00366         bin_min = uves_min_int(bin_min, uves_round_double(wstart/wavestep));
00367         bin_max = uves_max_int(bin_max, uves_round_double(wend  /wavestep));
00368     }
00369     total_bins = (bin_max - bin_min) + 1;
00370 
00371     uves_msg_debug("Merging orders into %d bins covering wavelengths %.3f - %.3f wlu", 
00372             total_bins, bin_min * wavestep, bin_max * wavestep);
00373 
00374     /* Initialize spectrum to zero and noise to negative */
00375     if(m_method == MERGE_NOAPPEND) {
00376       merged        = cpl_image_new(total_bins, n_traces*norders, type);
00377       *merged_noise = cpl_image_new(total_bins, n_traces*norders, type);
00378     } else {
00379       merged        = cpl_image_new(total_bins, n_traces, type);
00380       *merged_noise = cpl_image_new(total_bins, n_traces, type);
00381     }
00382     cpl_image_add_scalar(*merged_noise, -1.0);
00383     //cpl_image_power(spectrum_noise,0.5);
00384     //cpl_image_multiply_scalar(spectrum_noise,0.25);
00385     /* Distribute input in output bins */
00386     for (order = 1; order <= norders; order++)
00387     {
00388         double wstart, wend;
00389         int wstart_bin, wend_bin;      /* In 1d space */
00390 
00391 
00392 
00393         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00394            "Error reading start wavelength for order #%d", order);
00395         
00396         check( wend = uves_pfits_get_wend(spectrum_header, order),
00397            "Error reading end wavelength for order #%d", order);
00398 
00399     //wstart+=delt1;
00400     //wend-=delt2;
00401         
00402         wstart_bin = uves_round_double(wstart/wavestep);
00403         wend_bin   = uves_round_double(wend/wavestep);
00404         delt1_bin  = uves_round_double(delt1/wavestep);
00405         delt2_bin  = uves_round_double(delt2/wavestep);
00406 
00407         
00408     int bin_min_ord = uves_round_double(wstart/wavestep);
00409     int bin_max_ord = uves_round_double(wend  /wavestep);
00410         int nbins_ord = (bin_max_ord - bin_min_ord) + 1;
00411       cpl_image* merged_ord=NULL;
00412       cpl_image * noise_ord=NULL;
00413 
00414     if(m_method == MERGE_NOAPPEND) {
00415       merged_ord = cpl_image_new(nbins_ord, n_traces, type);
00416       noise_ord = cpl_image_new(nbins_ord, n_traces, type);
00417     }
00418 
00419         //if(order>1 && order<norders) {
00420     //  med_noise=cpl_image_get_median_window(spectrum_noise,
00421     //                  1,order,ny,order);
00422     //} else {
00423     //  med_noise=cpl_image_get_median(spectrum_noise);
00424     //}
00425         /* Loop over spatial traces (only 1 trace, unless extraction was 2d) */
00426         for (trace = 1; trace <= n_traces; trace++)
00427         {
00428       int merged_row = 0;
00429       int spectrum_row = (order - 1)*n_traces + trace;
00430       if(m_method == MERGE_NOAPPEND) {
00431         merged_row = (order - 1)*n_traces + trace;
00432       } else {
00433         merged_row = trace;
00434 
00435       }
00436             int rel_bin;                   /* Counting columns in input spectrum */
00437             
00438             for (rel_bin = 1+delt1_bin; 
00439                  (rel_bin <= wend_bin - wstart_bin + 1-delt2_bin) &&
00440                  (rel_bin <(spectrum_sx*spectrum_sy+1-(spectrum_row-1)*nbins));
00441                  rel_bin++)
00442             {
00443                 double flux, noise;
00444                 double current_flux, new_flux;
00445                 double current_noise, new_noise;
00446                 double weight;
00447                 int pis_rejected, noise_rejected;
00448                 
00449                 /* merged_bin = (offset of order)  +  (offset inside order) */
00450                 int merged_bin = (wstart_bin - bin_min) + rel_bin;
00451                 int merged_bin_ord = rel_bin;
00452                 
00453                 passure(1 <= merged_bin && merged_bin <= total_bins,
00454                     "%d %d %d", rel_bin, merged_bin, total_bins);
00455                 
00456                 /* This is slow:
00457                    check( flux  = cpl_image_get(spectrum      , 
00458                           rel_bin, spectrum_row, &pis_rejected);
00459                    noise = cpl_image_get(spectrum_noise, rel_bin, 
00460                     spectrum_row, &noise_rejected),
00461                    "Error reading input spectrum");
00462                 */
00463                 
00464                 if (type == CPL_TYPE_DOUBLE) {
00465                     flux  = spectrum_data_double[(rel_bin-1) + (spectrum_row-1) * nbins];
00466                     noise = noise_data_double   [(rel_bin-1) + (spectrum_row-1) * nbins];
00467 
00468                 }
00469                 else {
00470                     flux  = spectrum_data_float[(rel_bin-1) + (spectrum_row-1) * nbins];
00471                     noise = noise_data_float   [(rel_bin-1) + (spectrum_row-1) * nbins];
00472                 }
00473 
00474                 pis_rejected   = spectrum_bad[(rel_bin-1) + (spectrum_row-1) * nbins];
00475                 noise_rejected = noise_bad   [(rel_bin-1) + (spectrum_row-1) * nbins];
00476                 
00477                 if (!pis_rejected && !noise_rejected)
00478                 {
00479 
00480           if(m_method == MERGE_NOAPPEND) {
00481                     check(( current_flux  = cpl_image_get(merged, 
00482                                                           merged_bin, 
00483                                                           merged_row, 
00484                               &pis_rejected),
00485                 current_noise = cpl_image_get(*merged_noise, 
00486                               merged_bin, 
00487                                                           merged_row, 
00488                               &pis_rejected)),
00489               "Error reading merged spetrum");
00490           } else {
00491                     check(( current_flux  = cpl_image_get(
00492                         merged      , merged_bin, trace, &pis_rejected),
00493                         current_noise = cpl_image_get(
00494                         *merged_noise, merged_bin, trace, &pis_rejected)),
00495                        "Error reading merged spetrum");
00496           }
00497           weight = 1/(noise*noise);
00498                     
00499                     /*
00500                      * Optimal formulas for Variance and Flux are
00501                      *
00502                      *   Vn = ( 1/sigma1^2 + ... +  1/sigmaN^2)^-1
00503                      *   Fn = (f1/sigma1^2 + ... + fN/sigmaN^2) * Vn
00504                      *
00505                      * Update by using these recurrence relations
00506                      *
00507                      *   Fn+1 = (Fn/Vn + fn+1/(sigma_{n+1})^2) * Vn+1  for n > 1
00508                      *   Vn+1 = (Vn^-1 + 1/(sigma_{n+1})^2)^-1  for n > 1
00509                      *
00510                      *
00511                      *  In the case of method = sum,
00512                      *
00513                      *  Vn = sigma1^2 + ... + sigmaN^2
00514                      *  Fn = f1 + ... + fN
00515                      *
00516                      */
00517                     
00518                     if (current_noise > 0)
00519                     {
00520                         if (m_method == MERGE_OPTIMAL)
00521                         {
00522                             new_noise  = 1/(current_noise*current_noise);
00523                             new_noise += weight;
00524                             new_noise  = 1/sqrt(new_noise);
00525                         }
00526                         else if (m_method == MERGE_SUM)
00527                         {
00528                             new_noise = sqrt(current_noise*current_noise
00529                                      + noise*noise);
00530                         }
00531                         else if (m_method == MERGE_NOAPPEND)
00532                         {
00533                             new_noise = current_noise;
00534                         }
00535                         else
00536                         {
00537                             /* Impossible */
00538                             passure( false, "%d", m_method);
00539                         }
00540                     }
00541                     else
00542                     {
00543                         /* First time in this bin */
00544                         new_noise = noise;
00545                     }
00546                     
00547                     if (current_noise > 0)
00548                     {
00549                         if (m_method == MERGE_OPTIMAL)
00550                         {
00551                             new_flux = (current_flux / 
00552                                 (current_noise*current_noise)
00553                                 + flux * weight) * 
00554                             (new_noise*new_noise);
00555                         }
00556                         else if (m_method == MERGE_SUM)
00557                         {
00558                             new_flux = current_flux + flux;
00559                         }
00560                         else if (m_method == MERGE_NOAPPEND)
00561               {
00562                             new_flux = flux;
00563               }
00564                         else
00565                         {
00566                             /* Impossible */
00567                             passure( false, "%d", m_method);
00568                         }
00569                     }
00570                     else
00571                     {
00572                         new_flux = flux;
00573                     }
00574                     
00575           if(m_method == MERGE_NOAPPEND) {
00576 
00577             /*
00578               uves_msg_warning("flux[%d,%d]=%g noise=%g",
00579                        merged_bin,merged_row,
00580                        new_flux,current_noise);
00581             */
00582                     check( cpl_image_set(
00583                      merged, 
00584                                          merged_bin, 
00585                                          merged_row, 
00586                                          new_flux),
00587                        "Error updating merged spectrum");
00588 
00589                     check( cpl_image_set(
00590                      *merged_noise, 
00591                                           merged_bin, 
00592                      merged_row, 
00593                                          new_noise),
00594                        "Error updating weights");
00595 
00596 
00597                     check( cpl_image_set(
00598                      merged_ord, 
00599                                          merged_bin_ord, 
00600                                          trace, 
00601                                          new_flux),
00602                        "Error updating merged spectrum");
00603 
00604                     check( cpl_image_set(
00605                      noise_ord, 
00606                                          merged_bin_ord, 
00607                                          trace, 
00608                                          new_noise),
00609                        "Error updating merged spectrum");
00610 
00611 
00612           } else {
00613                     check( cpl_image_set(
00614                            merged      , merged_bin, trace, new_flux),
00615                        "Error updating merged spectrum");
00616                     check( cpl_image_set(
00617                            *merged_noise, merged_bin, trace, new_noise),
00618                        "Error updating weights");
00619           }
00620 /*            uves_msg("Input flux = %e +- %e ;  
00621             Binned flux changed from %e +- %e to %e +- %e",
00622             flux, noise,
00623             current_flux, current_noise, new_flux, new_noise);*/
00624                     
00625                 } /* If pixel is good ... */
00626 
00627             } /* For each input bin */
00628 
00629         }/* For trace ... */
00630 
00631 
00632     if (merged_header == NULL)
00633         {
00634            uves_free_propertylist(merged_header);
00635            check( *merged_header = uves_initialize_image_header(
00636                      "WAVELENGTH", (n_traces > 1) ? "PIXEL" : " ", "FLUX",
00637                      bin_min_ord * wavestep, 1.0,
00638                      1.0, 1.0,
00639                      wavestep, 1.0),
00640                   "Error initializing merged spectrum header");
00641         }
00642 
00643         if(m_method == MERGE_NOAPPEND) {
00644            filename=uves_sprintf("merged_data_noappend_%s.fits",
00645                            uves_chip_tostring_upper(chip));
00646            image_1d = cpl_vector_wrap(cpl_image_get_size_x(merged_ord),
00647                                       cpl_image_get_data_double(merged_ord));
00648            uves_free_propertylist(&hext);
00649            hext=uves_propertylist_new();
00650            uves_propertylist_append_double(hext,"CRVAL1",wstart-delt1);
00651            uves_propertylist_append_double(hext,"CDELT1",wavestep);
00652            uves_propertylist_append_double(hext,"CRPIX1",0);
00653 
00654            if(order==1) {
00655             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00656                                     CPL_IO_DEFAULT);
00657            } else {
00658             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00659                                     CPL_IO_EXTEND);
00660            }
00661            cpl_vector_unwrap(image_1d);
00662 
00663            image_1d = cpl_vector_wrap(cpl_image_get_size_x(noise_ord),
00664                                       cpl_image_get_data_double(noise_ord));
00665 
00666            uves_free(filename);
00667       
00668            filename=uves_sprintf("merged_sigma_noappend_%s.fits",
00669                                  uves_chip_tostring_upper(chip));
00670            if(order==1) {
00671             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00672                                     CPL_IO_DEFAULT);
00673            } else {
00674             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00675                                     CPL_IO_EXTEND);
00676            }
00677            cpl_vector_unwrap(image_1d);
00678 
00679            uves_free(filename);
00680            uves_free_image(&merged_ord);
00681            uves_free_image(&noise_ord);
00682            uves_free_propertylist(&hext);
00683            uves_free_propertylist(merged_header);
00684         }
00685 
00686     }/* For order ... */
00687     
00688     /* Undefined bins have  (flux, noise) = (0, -1)  (the initial values).
00689      * Set to (flux, noise) = (0, 1)
00690      */
00691 
00692 /* Here commented out piece of code to be used eventually to have
00693    noappend files files as products
00694     if(m_method == MERGE_NOAPPEND) {
00695        cpl_frame* mdata_noappend=NULL;
00696        cpl_frame* msigma_noappend=NULL;
00697        mdata_noappend=cpl_frame_new();
00698        msigma_noappend=cpl_frame_new();
00699        cpl_frame_set_group(mdata_noappend,CPL_FRAME_GROUP_PRODUCT);
00700        cpl_frame_set_type(mdata_noappend,CPL_FRAME_TYPE_IMAGE);
00701        cpl_frame_set_level(mdata_noappend,CPL_FRAME_LEVEL_FINAL);
00702 
00703        tag=uves_sprintf("MERGED_SCI_NOAPPEND_%s",
00704                              uves_chip_tostring_upper(chip));
00705        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00706        cpl_frame_set_tag(mdata_noappend,tag);
00707        cpl_frame_set_filename(mdata_noappend,filename);
00708        uves_free(filename);
00709        uves_free(tag);
00710 
00711        cpl_frame_set_group(msigma_noappend,CPL_FRAME_GROUP_PRODUCT);
00712        cpl_frame_set_type(msigma_noappend,CPL_FRAME_TYPE_IMAGE);
00713        cpl_frame_set_level(msigma_noappend,CPL_FRAME_LEVEL_FINAL);
00714 
00715        tag=uves_sprintf("MERGED_ERR_NOAPPEND_%s",
00716                              uves_chip_tostring_upper(chip));
00717        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00718        cpl_frame_set_tag(msigma_noappend,tag);
00719        cpl_frame_set_filename(msigma_noappend,filename);
00720 
00721        uves_free_frame(&mdata_noappend);
00722        uves_free_frame(&msigma_noappend);
00723        uves_free(filename);
00724        uves_free(tag);
00725 
00726     }
00727 */
00728     check( cpl_image_threshold(*merged_noise, 
00729                    0, DBL_MAX,        /* Outside this interval */
00730                    1, 1),             /* Set to these values   */
00731        "Error setting undefined noise");
00732  
00733     
00734     if (merged_header != NULL)
00735     {
00736         check( *merged_header = uves_initialize_image_header(
00737                "WAVELENGTH [Ang]", (n_traces > 1) ? "PIXEL" : " ", "ADU",
00738                bin_min * wavestep, 1.0,
00739                1.0, 1.0,
00740                wavestep, 1.0),
00741            "Error initializing merged spectrum header");
00742     }
00743  
00744     
00745   cleanup:
00746     return merged;
00747 }
00748 
00749 /*---------------------------------------------------------------------------*/
00759 /*---------------------------------------------------------------------------*/
00760 merge_method
00761 uves_get_merge_method(const cpl_parameterlist *parameters, 
00762                       const char *context, 
00763                       const char *subcontext)
00764 {
00765     const char *mm = "";
00766     merge_method result = 0;
00767     
00768     check( uves_get_parameter(parameters, context, subcontext, "merge", CPL_TYPE_STRING, &mm),
00769        "Could not read parameter");
00770     
00771     if      (strcmp(mm, "optimal") == 0) result = MERGE_OPTIMAL;
00772     else if (strcmp(mm, "sum"    ) == 0) result = MERGE_SUM;
00773     else if (strcmp(mm, "noappend") == 0) result = MERGE_NOAPPEND;
00774     else
00775     {
00776         assure(false, CPL_ERROR_ILLEGAL_INPUT, "No such merging method: '%s'", mm);
00777     }
00778     
00779   cleanup:
00780     return result;
00781 }
00782     
00783 

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