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: 2011/12/08 14:03:09 $
00024  * $Revision: 1.61 $
00025  * $Name: uves-4_9_15 $
00026  * $Log: uves_merge.c,v $
00027  * Revision 1.61  2011/12/08 14:03:09  amodigli
00028  * Fix warnings with CPL6
00029  *
00030  * Revision 1.60  2010/12/16 16:57:40  amodigli
00031  * fixed compiler warnings
00032  *
00033  * Revision 1.59  2010/12/08 11:07:59  amodigli
00034  * added chip parameter to uves_merge_orders() to have proper filenames. Fixed content err data for noappend case
00035  *
00036  * Revision 1.58  2010/09/27 06:32:22  amodigli
00037  * fixed mem leaks
00038  *
00039  * Revision 1.57  2010/09/24 09:32:04  amodigli
00040  * put back QFITS dependency to fix problem spot by NRI on FIBER mode (with MIDAS calibs) data
00041  *
00042  * Revision 1.55  2010/06/07 09:48:00  amodigli
00043  * changed units: A-->Ang, FLUX-->ADU
00044  *
00045  * Revision 1.54  2010/06/01 16:06:55  amodigli
00046  * added unit [A] to reduced product
00047  *
00048  * Revision 1.53  2008/09/29 06:57:41  amodigli
00049  * add #include <string.h>
00050  *
00051  * Revision 1.52  2008/09/27 16:05:12  amodigli
00052  * fixed bug using delta parmeters
00053  *
00054  * Revision 1.51  2008/09/23 11:32:39  amodigli
00055  * added check on array upper bound access to fix DFS05803
00056  *
00057  * Revision 1.50  2008/08/29 09:52:39  amodigli
00058  * fixed compiler warning
00059  *
00060  * Revision 1.49  2008/06/26 08:30:38  amodigli
00061  * fixed bug in setting delta
00062  *
00063  * Revision 1.48  2008/06/11 14:42:50  amodigli
00064  * fixed seg fault
00065  *
00066  * Revision 1.45  2008/03/04 07:35:31  amodigli
00067  * generate spectra of each order only if NOAPPEND
00068  *
00069  * Revision 1.44  2008/02/21 07:50:38  amodigli
00070  * added method NOAPPEND
00071  *
00072  * Revision 1.43  2007/08/21 13:08:26  jmlarsen
00073  * Removed irplib_access module, largely deprecated by CPL-4
00074  *
00075  * Revision 1.42  2007/06/21 11:28:57  jmlarsen
00076  * Added support for type float (for FLAMES)
00077  *
00078  * Revision 1.41  2007/06/06 08:17:33  amodigli
00079  * replace tab with 4 spaces
00080  *
00081  * Revision 1.40  2007/05/03 15:21:13  jmlarsen
00082  * Decreased output message verbosity
00083  *
00084  * Revision 1.39  2007/04/24 12:50:29  jmlarsen
00085  * Replaced cpl_propertylist -> uves_propertylist which is much faster
00086  *
00087  * Revision 1.38  2007/02/09 08:57:54  jmlarsen
00088  * Include <float.h>
00089  *
00090  * Revision 1.37  2007/02/09 08:14:16  jmlarsen
00091  * Do not use CPL_PIXEL_MAXVAL which works only for integer images
00092  *
00093  * Revision 1.36  2007/02/08 07:34:28  jmlarsen
00094  * Minor doc change
00095  *
00096  * Revision 1.35  2006/11/15 15:02:14  jmlarsen
00097  * Implemented const safe workarounds for CPL functions
00098  *
00099  * Revision 1.33  2006/11/15 14:04:08  jmlarsen
00100  * Removed non-const version of parameterlist_get_first/last/next which is already
00101  * in CPL, added const-safe wrapper, unwrapper and deallocator functions
00102  *
00103  * Revision 1.32  2006/11/13 14:23:55  jmlarsen
00104  * Removed workarounds for CPL const bugs
00105  *
00106  * Revision 1.31  2006/11/06 15:19:41  jmlarsen
00107  * Removed unused include directives
00108  *
00109  * Revision 1.30  2006/09/11 14:00:11  jmlarsen
00110  * Minor documentation change
00111  *
00112  * Revision 1.29  2006/08/17 13:56:53  jmlarsen
00113  * Reduced max line length
00114  *
00115  * Revision 1.28  2006/08/17 09:16:47  jmlarsen
00116  * Removed CPL2 code
00117  *
00118  * Revision 1.27  2006/08/11 14:37:59  jmlarsen
00119  * Added input validation
00120  *
00121  * Revision 1.26  2006/08/10 10:50:12  jmlarsen
00122  * Removed workaround for cpl_image_get_bpm
00123  *
00124  * Revision 1.25  2006/07/03 13:16:42  jmlarsen
00125  * Reduced number of significant digits in message
00126  *
00127  * Revision 1.24  2006/04/06 08:38:56  jmlarsen
00128  * Changed char* -> const char* for static string
00129  *
00130  * Revision 1.23  2006/03/03 13:54:11  jmlarsen
00131  * Changed syntax of check macro
00132  *
00133  * Revision 1.22  2006/02/03 07:46:30  jmlarsen
00134  * Moved recipe implementations to ./uves directory
00135  *
00136  * Revision 1.21  2006/01/31 08:24:29  jmlarsen
00137  * Wrapper for cpl_image_get_bpm
00138  *
00139  * Revision 1.20  2006/01/25 16:13:20  jmlarsen
00140  * Changed interface of gauss.fitting routine
00141  *
00142  * Revision 1.19  2005/12/19 16:17:56  jmlarsen
00143  * Replaced bool -> int
00144  *
00145  * Revision 1.18  2005/12/16 14:22:23  jmlarsen
00146  * Removed midas test data; Added sof files
00147  *
00148  * Revision 1.17  2005/11/24 15:09:06  jmlarsen
00149  * Implemented 2d extraction/rebinning/merging
00150  *
00151  * Revision 1.16  2005/11/24 11:54:46  jmlarsen
00152  * Added support for CPL 3 interface
00153  *
00154  * Revision 1.15  2005/11/18 10:52:06  jmlarsen
00155  * Split into optimal/sum merge methods
00156  *
00157  * Revision 1.14  2005/11/11 13:18:54  jmlarsen
00158  * Reorganized code, renamed source files
00159  *
00160  */
00161 
00162 #ifdef HAVE_CONFIG_H
00163 #  include <config.h>
00164 #endif
00165 
00166 /*----------------------------------------------------------------------------*/
00172 /*----------------------------------------------------------------------------*/
00176 /*-----------------------------------------------------------------------------
00177                                 Includes
00178  -----------------------------------------------------------------------------*/
00179 
00180 #include <uves_merge.h>
00181 
00182 #include <uves_pfits.h>
00183 #include <uves_utils.h>
00184 #include <uves_utils_wrappers.h>
00185 #include <uves_dump.h>
00186 #include <uves_dfs.h>
00187 #include <uves_error.h>
00188 
00189 #include <cpl.h>
00190 #include <float.h>
00191 #include <string.h>
00192 /*-----------------------------------------------------------------------------
00193                             Functions prototypes
00194  ----------------------------------------------------------------------------*/
00195 
00196 /*-----------------------------------------------------------------------------
00197                             Implementation
00198  ----------------------------------------------------------------------------*/
00199 
00200 /*---------------------------------------------------------------------------*/
00227 /*---------------------------------------------------------------------------*/
00228 
00229 cpl_image *
00230 uves_merge_orders(const cpl_image *spectrum, 
00231                   const cpl_image *spectrum_noise,
00232                   const uves_propertylist *spectrum_header,
00233                   merge_method m_method,
00234                   int n_traces,
00235                   uves_propertylist **merged_header,
00236                   const double delt1, 
00237                   const double delt2,
00238                   enum uves_chip chip,
00239                   cpl_image **merged_noise)
00240 {
00241     cpl_image *merged = NULL;    /* Result */
00242 
00243     const double *spectrum_data_double = NULL;
00244     const float  *spectrum_data_float  = NULL;
00245     const cpl_mask *spectrum_badmap    = NULL;
00246     const cpl_binary *spectrum_bad     = NULL;
00247 
00248     const double *noise_data_double = NULL;
00249     const float *noise_data_float   = NULL;
00250     const cpl_mask *noise_badmap    = NULL;
00251     const cpl_binary *noise_bad     = NULL;
00252     cpl_type type;               /* input/output images type */
00253 
00254     int nbins, ny, norders;          /* Input image size. ny = norders*n_traces */
00255     double wavestep;
00256     int bin_min = 0, bin_max = 0;    /* wavelength of min/max bin in units of 'wavestep' */
00257     int total_bins;
00258     int order, trace;
00259     int spectrum_sx=0;
00260     int spectrum_sy=0;
00261     double delt1_bin=0;
00262     double delt2_bin=0;
00263     char* filename=NULL;
00264 
00265     cpl_vector* image_1d=NULL;
00266     uves_propertylist* hext=NULL;
00267     //double med_noise=0;
00268     passure( spectrum != NULL, " ");
00269     passure( spectrum_noise != NULL, " ");
00270     passure( spectrum_header != NULL, " ");
00271     passure( merged_header != NULL, " ");
00272     passure( merged_noise != NULL, " ");
00273 
00274     assure( m_method == MERGE_OPTIMAL || 
00275             m_method == MERGE_SUM || 
00276             m_method == MERGE_NOAPPEND, 
00277             CPL_ERROR_ILLEGAL_INPUT,
00278             "Unknown merge method: %d", m_method);
00279     
00280     assure( cpl_image_get_type(spectrum) == CPL_TYPE_DOUBLE ||
00281             cpl_image_get_type(spectrum) == CPL_TYPE_FLOAT,
00282             CPL_ERROR_TYPE_MISMATCH,
00283             "Spectrum must have type double or float. It is '%s'",
00284             uves_tostring_cpl_type(cpl_image_get_type(spectrum)));
00285     
00286     assure( cpl_image_get_type(spectrum_noise) == CPL_TYPE_DOUBLE ||
00287             cpl_image_get_type(spectrum_noise) == CPL_TYPE_FLOAT,
00288             CPL_ERROR_TYPE_MISMATCH,
00289             "Spectrum noise must have type double. It is '%s'",
00290             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)));
00291 
00292     assure( cpl_image_get_type(spectrum) ==
00293             cpl_image_get_type(spectrum_noise),
00294             CPL_ERROR_TYPE_MISMATCH,
00295             "Spectrum and spectrum noise must have same type. They are "
00296             "%s and %s, respectively",
00297             uves_tostring_cpl_type(cpl_image_get_type(spectrum)),
00298             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)) );
00299 
00300     type = cpl_image_get_type(spectrum);
00301 
00302     /* Read input spectrum geometry */
00303     nbins           = cpl_image_get_size_x(spectrum);
00304     ny              = cpl_image_get_size_y(spectrum);
00305 
00306     assure( cpl_image_get_size_x(spectrum_noise) == nbins &&
00307             cpl_image_get_size_y(spectrum_noise) == ny,
00308             CPL_ERROR_INCOMPATIBLE_INPUT,
00309             "Incompatible spectrum/noise image sizes: %"CPL_SIZE_FORMAT"x%" CPL_SIZE_FORMAT " vs. %" CPL_SIZE_FORMAT "x%" CPL_SIZE_FORMAT "",
00310             nbins, ny,
00311             cpl_image_get_size_x(spectrum_noise),
00312             cpl_image_get_size_y(spectrum_noise) );
00313     
00314     assure( ny % n_traces == 0, CPL_ERROR_INCOMPATIBLE_INPUT,
00315             "Spectrum image height (%d) is not a multiple of "
00316             "the number of traces (%d). Confused, bailing out",
00317             ny, n_traces);
00318 
00319     norders         = ny / n_traces;
00320     
00321     check( wavestep = uves_pfits_get_cdelt1(spectrum_header),
00322        "Error reading bin width");
00323 
00324     /* Get data pointers (for efficiency) */
00325    
00326     if (type == CPL_TYPE_DOUBLE) {
00327         spectrum_data_double   = cpl_image_get_data_double_const(spectrum);
00328     }
00329     else {
00330         spectrum_data_float   = cpl_image_get_data_float_const(spectrum);
00331     }
00332 
00333     spectrum_sx=cpl_image_get_size_x(spectrum);
00334     spectrum_sy=cpl_image_get_size_y(spectrum);
00335 
00336     spectrum_badmap = cpl_image_get_bpm_const(spectrum);
00337     spectrum_bad    = cpl_mask_get_data_const(spectrum_badmap);
00338     
00339     if (type == CPL_TYPE_DOUBLE) {
00340         noise_data_double = cpl_image_get_data_double_const(spectrum_noise);        
00341     }
00342     else {
00343         noise_data_float  = cpl_image_get_data_float_const(spectrum_noise);
00344     }
00345     noise_badmap = cpl_image_get_bpm_const(spectrum_noise);
00346     noise_bad    = cpl_mask_get_data_const(noise_badmap);
00347     uves_msg("delt1=%f delt2=%f",delt1,delt2);
00348     /* Read max/min lambda */
00349     for (order = 1; order <= norders; order++)
00350     {
00351         double wstart, wend;
00352         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00353            "Error reading start wavelength for order #%d", order);
00354 
00355         check( wend = uves_pfits_get_wend(spectrum_header, order),
00356            "Error reading end wavelength for order #%d", order);
00357         
00358         uves_msg_debug("Order #%d: wstart - wend = %f - %f wlu", order, wstart, wend);
00359 
00360     //wstart+=delt1;
00361     //wend-=delt2;
00362 
00363         if (order == 1)
00364         {
00365             bin_min = uves_round_double(wstart/wavestep);
00366             bin_max = uves_round_double(wend  /wavestep);
00367         }
00368         
00369         bin_min = uves_min_int(bin_min, uves_round_double(wstart/wavestep));
00370         bin_max = uves_max_int(bin_max, uves_round_double(wend  /wavestep));
00371     }
00372     total_bins = (bin_max - bin_min) + 1;
00373 
00374     uves_msg_debug("Merging orders into %d bins covering wavelengths %.3f - %.3f wlu", 
00375             total_bins, bin_min * wavestep, bin_max * wavestep);
00376 
00377     /* Initialize spectrum to zero and noise to negative */
00378     if(m_method == MERGE_NOAPPEND) {
00379       merged        = cpl_image_new(total_bins, n_traces*norders, type);
00380       *merged_noise = cpl_image_new(total_bins, n_traces*norders, type);
00381     } else {
00382       merged        = cpl_image_new(total_bins, n_traces, type);
00383       *merged_noise = cpl_image_new(total_bins, n_traces, type);
00384     }
00385     cpl_image_add_scalar(*merged_noise, -1.0);
00386     //cpl_image_power(spectrum_noise,0.5);
00387     //cpl_image_multiply_scalar(spectrum_noise,0.25);
00388     /* Distribute input in output bins */
00389     for (order = 1; order <= norders; order++)
00390     {
00391         double wstart, wend;
00392         int wstart_bin, wend_bin;      /* In 1d space */
00393 
00394 
00395 
00396         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00397            "Error reading start wavelength for order #%d", order);
00398         
00399         check( wend = uves_pfits_get_wend(spectrum_header, order),
00400            "Error reading end wavelength for order #%d", order);
00401 
00402     //wstart+=delt1;
00403     //wend-=delt2;
00404         
00405         wstart_bin = uves_round_double(wstart/wavestep);
00406         wend_bin   = uves_round_double(wend/wavestep);
00407         delt1_bin  = uves_round_double(delt1/wavestep);
00408         delt2_bin  = uves_round_double(delt2/wavestep);
00409 
00410         
00411     int bin_min_ord = uves_round_double(wstart/wavestep);
00412     int bin_max_ord = uves_round_double(wend  /wavestep);
00413         int nbins_ord = (bin_max_ord - bin_min_ord) + 1;
00414       cpl_image* merged_ord=NULL;
00415       cpl_image * noise_ord=NULL;
00416 
00417     if(m_method == MERGE_NOAPPEND) {
00418       merged_ord = cpl_image_new(nbins_ord, n_traces, type);
00419       noise_ord = cpl_image_new(nbins_ord, n_traces, type);
00420     }
00421 
00422         //if(order>1 && order<norders) {
00423     //  med_noise=cpl_image_get_median_window(spectrum_noise,
00424     //                  1,order,ny,order);
00425     //} else {
00426     //  med_noise=cpl_image_get_median(spectrum_noise);
00427     //}
00428         /* Loop over spatial traces (only 1 trace, unless extraction was 2d) */
00429         for (trace = 1; trace <= n_traces; trace++)
00430         {
00431       int merged_row = 0;
00432       int spectrum_row = (order - 1)*n_traces + trace;
00433       if(m_method == MERGE_NOAPPEND) {
00434         merged_row = (order - 1)*n_traces + trace;
00435       } else {
00436         merged_row = trace;
00437 
00438       }
00439             int rel_bin;                   /* Counting columns in input spectrum */
00440             
00441             for (rel_bin = 1+delt1_bin; 
00442                  (rel_bin <= wend_bin - wstart_bin + 1-delt2_bin) &&
00443                  (rel_bin <(spectrum_sx*spectrum_sy+1-(spectrum_row-1)*nbins));
00444                  rel_bin++)
00445             {
00446                 double flux, noise;
00447                 double current_flux, new_flux;
00448                 double current_noise, new_noise;
00449                 double weight;
00450                 int pis_rejected, noise_rejected;
00451                 
00452                 /* merged_bin = (offset of order)  +  (offset inside order) */
00453                 int merged_bin = (wstart_bin - bin_min) + rel_bin;
00454                 int merged_bin_ord = rel_bin;
00455                 
00456                 passure(1 <= merged_bin && merged_bin <= total_bins,
00457                     "%d %d %d", rel_bin, merged_bin, total_bins);
00458                 
00459                 /* This is slow:
00460                    check( flux  = cpl_image_get(spectrum      , 
00461                           rel_bin, spectrum_row, &pis_rejected);
00462                    noise = cpl_image_get(spectrum_noise, rel_bin, 
00463                     spectrum_row, &noise_rejected),
00464                    "Error reading input spectrum");
00465                 */
00466                 
00467                 if (type == CPL_TYPE_DOUBLE) {
00468                     flux  = spectrum_data_double[(rel_bin-1) + (spectrum_row-1) * nbins];
00469                     noise = noise_data_double   [(rel_bin-1) + (spectrum_row-1) * nbins];
00470 
00471                 }
00472                 else {
00473                     flux  = spectrum_data_float[(rel_bin-1) + (spectrum_row-1) * nbins];
00474                     noise = noise_data_float   [(rel_bin-1) + (spectrum_row-1) * nbins];
00475                 }
00476 
00477                 pis_rejected   = spectrum_bad[(rel_bin-1) + (spectrum_row-1) * nbins];
00478                 noise_rejected = noise_bad   [(rel_bin-1) + (spectrum_row-1) * nbins];
00479                 
00480                 if (!pis_rejected && !noise_rejected)
00481                 {
00482 
00483           if(m_method == MERGE_NOAPPEND) {
00484                     check(( current_flux  = cpl_image_get(merged, 
00485                                                           merged_bin, 
00486                                                           merged_row, 
00487                               &pis_rejected),
00488                 current_noise = cpl_image_get(*merged_noise, 
00489                               merged_bin, 
00490                                                           merged_row, 
00491                               &pis_rejected)),
00492               "Error reading merged spetrum");
00493           } else {
00494                     check(( current_flux  = cpl_image_get(
00495                         merged      , merged_bin, trace, &pis_rejected),
00496                         current_noise = cpl_image_get(
00497                         *merged_noise, merged_bin, trace, &pis_rejected)),
00498                        "Error reading merged spetrum");
00499           }
00500           weight = 1/(noise*noise);
00501                     
00502                     /*
00503                      * Optimal formulas for Variance and Flux are
00504                      *
00505                      *   Vn = ( 1/sigma1^2 + ... +  1/sigmaN^2)^-1
00506                      *   Fn = (f1/sigma1^2 + ... + fN/sigmaN^2) * Vn
00507                      *
00508                      * Update by using these recurrence relations
00509                      *
00510                      *   Fn+1 = (Fn/Vn + fn+1/(sigma_{n+1})^2) * Vn+1  for n > 1
00511                      *   Vn+1 = (Vn^-1 + 1/(sigma_{n+1})^2)^-1  for n > 1
00512                      *
00513                      *
00514                      *  In the case of method = sum,
00515                      *
00516                      *  Vn = sigma1^2 + ... + sigmaN^2
00517                      *  Fn = f1 + ... + fN
00518                      *
00519                      */
00520                     
00521                     if (current_noise > 0)
00522                     {
00523                         if (m_method == MERGE_OPTIMAL)
00524                         {
00525                             new_noise  = 1/(current_noise*current_noise);
00526                             new_noise += weight;
00527                             new_noise  = 1/sqrt(new_noise);
00528                         }
00529                         else if (m_method == MERGE_SUM)
00530                         {
00531                             new_noise = sqrt(current_noise*current_noise
00532                                      + noise*noise);
00533                         }
00534                         else if (m_method == MERGE_NOAPPEND)
00535                         {
00536                             new_noise = current_noise;
00537                         }
00538                         else
00539                         {
00540                             /* Impossible */
00541                             passure( false, "%d", m_method);
00542                         }
00543                     }
00544                     else
00545                     {
00546                         /* First time in this bin */
00547                         new_noise = noise;
00548                     }
00549                     
00550                     if (current_noise > 0)
00551                     {
00552                         if (m_method == MERGE_OPTIMAL)
00553                         {
00554                             new_flux = (current_flux / 
00555                                 (current_noise*current_noise)
00556                                 + flux * weight) * 
00557                             (new_noise*new_noise);
00558                         }
00559                         else if (m_method == MERGE_SUM)
00560                         {
00561                             new_flux = current_flux + flux;
00562                         }
00563                         else if (m_method == MERGE_NOAPPEND)
00564               {
00565                             new_flux = flux;
00566               }
00567                         else
00568                         {
00569                             /* Impossible */
00570                             passure( false, "%d", m_method);
00571                         }
00572                     }
00573                     else
00574                     {
00575                         new_flux = flux;
00576                     }
00577                     
00578           if(m_method == MERGE_NOAPPEND) {
00579 
00580             /*
00581               uves_msg_warning("flux[%d,%d]=%g noise=%g",
00582                        merged_bin,merged_row,
00583                        new_flux,current_noise);
00584             */
00585                     check( cpl_image_set(
00586                      merged, 
00587                                          merged_bin, 
00588                                          merged_row, 
00589                                          new_flux),
00590                        "Error updating merged spectrum");
00591 
00592                     check( cpl_image_set(
00593                      *merged_noise, 
00594                                           merged_bin, 
00595                      merged_row, 
00596                                          new_noise),
00597                        "Error updating weights");
00598 
00599 
00600                     check( cpl_image_set(
00601                      merged_ord, 
00602                                          merged_bin_ord, 
00603                                          trace, 
00604                                          new_flux),
00605                        "Error updating merged spectrum");
00606 
00607                     check( cpl_image_set(
00608                      noise_ord, 
00609                                          merged_bin_ord, 
00610                                          trace, 
00611                                          new_noise),
00612                        "Error updating merged spectrum");
00613 
00614 
00615           } else {
00616                     check( cpl_image_set(
00617                            merged      , merged_bin, trace, new_flux),
00618                        "Error updating merged spectrum");
00619                     check( cpl_image_set(
00620                            *merged_noise, merged_bin, trace, new_noise),
00621                        "Error updating weights");
00622           }
00623 /*            uves_msg("Input flux = %e +- %e ;  
00624             Binned flux changed from %e +- %e to %e +- %e",
00625             flux, noise,
00626             current_flux, current_noise, new_flux, new_noise);*/
00627                     
00628                 } /* If pixel is good ... */
00629 
00630             } /* For each input bin */
00631 
00632         }/* For trace ... */
00633 
00634 
00635     if (merged_header == NULL)
00636         {
00637            uves_free_propertylist(merged_header);
00638            check( *merged_header = uves_initialize_image_header(
00639                      "WAVELENGTH", (n_traces > 1) ? "PIXEL" : " ", "FLUX",
00640                      bin_min_ord * wavestep, 1.0,
00641                      1.0, 1.0,
00642                      wavestep, 1.0),
00643                   "Error initializing merged spectrum header");
00644         }
00645 
00646         if(m_method == MERGE_NOAPPEND) {
00647            filename=uves_sprintf("merged_data_noappend_%s.fits",
00648                            uves_chip_tostring_upper(chip));
00649            image_1d = cpl_vector_wrap(cpl_image_get_size_x(merged_ord),
00650                                       cpl_image_get_data_double(merged_ord));
00651            uves_free_propertylist(&hext);
00652            hext=uves_propertylist_new();
00653            uves_propertylist_append_double(hext,"CRVAL1",wstart-delt1);
00654            uves_propertylist_append_double(hext,"CDELT1",wavestep);
00655            uves_propertylist_append_double(hext,"CRPIX1",0);
00656 
00657            if(order==1) {
00658             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00659                                     CPL_IO_DEFAULT);
00660            } else {
00661             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00662                                     CPL_IO_EXTEND);
00663            }
00664            cpl_vector_unwrap(image_1d);
00665 
00666            image_1d = cpl_vector_wrap(cpl_image_get_size_x(noise_ord),
00667                                       cpl_image_get_data_double(noise_ord));
00668 
00669            uves_free(filename);
00670       
00671            filename=uves_sprintf("merged_sigma_noappend_%s.fits",
00672                                  uves_chip_tostring_upper(chip));
00673            if(order==1) {
00674             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00675                                     CPL_IO_DEFAULT);
00676            } else {
00677             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00678                                     CPL_IO_EXTEND);
00679            }
00680            cpl_vector_unwrap(image_1d);
00681 
00682            uves_free(filename);
00683            uves_free_image(&merged_ord);
00684            uves_free_image(&noise_ord);
00685            uves_free_propertylist(&hext);
00686            uves_free_propertylist(merged_header);
00687         }
00688 
00689     }/* For order ... */
00690     
00691     /* Undefined bins have  (flux, noise) = (0, -1)  (the initial values).
00692      * Set to (flux, noise) = (0, 1)
00693      */
00694 
00695 /* Here commented out piece of code to be used eventually to have
00696    noappend files files as products
00697     if(m_method == MERGE_NOAPPEND) {
00698        cpl_frame* mdata_noappend=NULL;
00699        cpl_frame* msigma_noappend=NULL;
00700        mdata_noappend=cpl_frame_new();
00701        msigma_noappend=cpl_frame_new();
00702        cpl_frame_set_group(mdata_noappend,CPL_FRAME_GROUP_PRODUCT);
00703        cpl_frame_set_type(mdata_noappend,CPL_FRAME_TYPE_IMAGE);
00704        cpl_frame_set_level(mdata_noappend,CPL_FRAME_LEVEL_FINAL);
00705 
00706        tag=uves_sprintf("MERGED_SCI_NOAPPEND_%s",
00707                              uves_chip_tostring_upper(chip));
00708        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00709        cpl_frame_set_tag(mdata_noappend,tag);
00710        cpl_frame_set_filename(mdata_noappend,filename);
00711        uves_free(filename);
00712        uves_free(tag);
00713 
00714        cpl_frame_set_group(msigma_noappend,CPL_FRAME_GROUP_PRODUCT);
00715        cpl_frame_set_type(msigma_noappend,CPL_FRAME_TYPE_IMAGE);
00716        cpl_frame_set_level(msigma_noappend,CPL_FRAME_LEVEL_FINAL);
00717 
00718        tag=uves_sprintf("MERGED_ERR_NOAPPEND_%s",
00719                              uves_chip_tostring_upper(chip));
00720        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00721        cpl_frame_set_tag(msigma_noappend,tag);
00722        cpl_frame_set_filename(msigma_noappend,filename);
00723 
00724        uves_free_frame(&mdata_noappend);
00725        uves_free_frame(&msigma_noappend);
00726        uves_free(filename);
00727        uves_free(tag);
00728 
00729     }
00730 */
00731     check( cpl_image_threshold(*merged_noise, 
00732                    0, DBL_MAX,        /* Outside this interval */
00733                    1, 1),             /* Set to these values   */
00734        "Error setting undefined noise");
00735  
00736     
00737     if (merged_header != NULL)
00738     {
00739         check( *merged_header = uves_initialize_image_header(
00740                "WAVELENGTH [Ang]", (n_traces > 1) ? "PIXEL" : " ", "ADU",
00741                bin_min * wavestep, 1.0,
00742                1.0, 1.0,
00743                wavestep, 1.0),
00744            "Error initializing merged spectrum header");
00745     }
00746  
00747     
00748   cleanup:
00749     return merged;
00750 }
00751 
00752 /*---------------------------------------------------------------------------*/
00762 /*---------------------------------------------------------------------------*/
00763 merge_method
00764 uves_get_merge_method(const cpl_parameterlist *parameters, 
00765                       const char *context, 
00766                       const char *subcontext)
00767 {
00768     const char *mm = "";
00769     merge_method result = 0;
00770     
00771     check( uves_get_parameter(parameters, context, subcontext, "merge", CPL_TYPE_STRING, &mm),
00772        "Could not read parameter");
00773     
00774     if      (strcmp(mm, "optimal") == 0) result = MERGE_OPTIMAL;
00775     else if (strcmp(mm, "sum"    ) == 0) result = MERGE_SUM;
00776     else if (strcmp(mm, "noappend") == 0) result = MERGE_NOAPPEND;
00777     else
00778     {
00779         assure(false, CPL_ERROR_ILLEGAL_INPUT, "No such merging method: '%s'", mm);
00780     }
00781     
00782   cleanup:
00783     return result;
00784 }
00785     
00786 

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