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: 2012/03/02 16:53:31 $
00024  * $Revision: 1.62 $
00025  * $Name: uves-5_0_0 $
00026  * $Log: uves_merge.c,v $
00027  * Revision 1.62  2012/03/02 16:53:31  amodigli
00028  * fixed warning related to upgrade to CPL6
00029  *
00030  * Revision 1.61  2011/12/08 14:03:09  amodigli
00031  * Fix warnings with CPL6
00032  *
00033  * Revision 1.60  2010/12/16 16:57:40  amodigli
00034  * fixed compiler warnings
00035  *
00036  * Revision 1.59  2010/12/08 11:07:59  amodigli
00037  * added chip parameter to uves_merge_orders() to have proper filenames. Fixed content err data for noappend case
00038  *
00039  * Revision 1.58  2010/09/27 06:32:22  amodigli
00040  * fixed mem leaks
00041  *
00042  * Revision 1.57  2010/09/24 09:32:04  amodigli
00043  * put back QFITS dependency to fix problem spot by NRI on FIBER mode (with MIDAS calibs) data
00044  *
00045  * Revision 1.55  2010/06/07 09:48:00  amodigli
00046  * changed units: A-->Ang, FLUX-->ADU
00047  *
00048  * Revision 1.54  2010/06/01 16:06:55  amodigli
00049  * added unit [A] to reduced product
00050  *
00051  * Revision 1.53  2008/09/29 06:57:41  amodigli
00052  * add #include <string.h>
00053  *
00054  * Revision 1.52  2008/09/27 16:05:12  amodigli
00055  * fixed bug using delta parmeters
00056  *
00057  * Revision 1.51  2008/09/23 11:32:39  amodigli
00058  * added check on array upper bound access to fix DFS05803
00059  *
00060  * Revision 1.50  2008/08/29 09:52:39  amodigli
00061  * fixed compiler warning
00062  *
00063  * Revision 1.49  2008/06/26 08:30:38  amodigli
00064  * fixed bug in setting delta
00065  *
00066  * Revision 1.48  2008/06/11 14:42:50  amodigli
00067  * fixed seg fault
00068  *
00069  * Revision 1.45  2008/03/04 07:35:31  amodigli
00070  * generate spectra of each order only if NOAPPEND
00071  *
00072  * Revision 1.44  2008/02/21 07:50:38  amodigli
00073  * added method NOAPPEND
00074  *
00075  * Revision 1.43  2007/08/21 13:08:26  jmlarsen
00076  * Removed irplib_access module, largely deprecated by CPL-4
00077  *
00078  * Revision 1.42  2007/06/21 11:28:57  jmlarsen
00079  * Added support for type float (for FLAMES)
00080  *
00081  * Revision 1.41  2007/06/06 08:17:33  amodigli
00082  * replace tab with 4 spaces
00083  *
00084  * Revision 1.40  2007/05/03 15:21:13  jmlarsen
00085  * Decreased output message verbosity
00086  *
00087  * Revision 1.39  2007/04/24 12:50:29  jmlarsen
00088  * Replaced cpl_propertylist -> uves_propertylist which is much faster
00089  *
00090  * Revision 1.38  2007/02/09 08:57:54  jmlarsen
00091  * Include <float.h>
00092  *
00093  * Revision 1.37  2007/02/09 08:14:16  jmlarsen
00094  * Do not use CPL_PIXEL_MAXVAL which works only for integer images
00095  *
00096  * Revision 1.36  2007/02/08 07:34:28  jmlarsen
00097  * Minor doc change
00098  *
00099  * Revision 1.35  2006/11/15 15:02:14  jmlarsen
00100  * Implemented const safe workarounds for CPL functions
00101  *
00102  * Revision 1.33  2006/11/15 14:04:08  jmlarsen
00103  * Removed non-const version of parameterlist_get_first/last/next which is already
00104  * in CPL, added const-safe wrapper, unwrapper and deallocator functions
00105  *
00106  * Revision 1.32  2006/11/13 14:23:55  jmlarsen
00107  * Removed workarounds for CPL const bugs
00108  *
00109  * Revision 1.31  2006/11/06 15:19:41  jmlarsen
00110  * Removed unused include directives
00111  *
00112  * Revision 1.30  2006/09/11 14:00:11  jmlarsen
00113  * Minor documentation change
00114  *
00115  * Revision 1.29  2006/08/17 13:56:53  jmlarsen
00116  * Reduced max line length
00117  *
00118  * Revision 1.28  2006/08/17 09:16:47  jmlarsen
00119  * Removed CPL2 code
00120  *
00121  * Revision 1.27  2006/08/11 14:37:59  jmlarsen
00122  * Added input validation
00123  *
00124  * Revision 1.26  2006/08/10 10:50:12  jmlarsen
00125  * Removed workaround for cpl_image_get_bpm
00126  *
00127  * Revision 1.25  2006/07/03 13:16:42  jmlarsen
00128  * Reduced number of significant digits in message
00129  *
00130  * Revision 1.24  2006/04/06 08:38:56  jmlarsen
00131  * Changed char* -> const char* for static string
00132  *
00133  * Revision 1.23  2006/03/03 13:54:11  jmlarsen
00134  * Changed syntax of check macro
00135  *
00136  * Revision 1.22  2006/02/03 07:46:30  jmlarsen
00137  * Moved recipe implementations to ./uves directory
00138  *
00139  * Revision 1.21  2006/01/31 08:24:29  jmlarsen
00140  * Wrapper for cpl_image_get_bpm
00141  *
00142  * Revision 1.20  2006/01/25 16:13:20  jmlarsen
00143  * Changed interface of gauss.fitting routine
00144  *
00145  * Revision 1.19  2005/12/19 16:17:56  jmlarsen
00146  * Replaced bool -> int
00147  *
00148  * Revision 1.18  2005/12/16 14:22:23  jmlarsen
00149  * Removed midas test data; Added sof files
00150  *
00151  * Revision 1.17  2005/11/24 15:09:06  jmlarsen
00152  * Implemented 2d extraction/rebinning/merging
00153  *
00154  * Revision 1.16  2005/11/24 11:54:46  jmlarsen
00155  * Added support for CPL 3 interface
00156  *
00157  * Revision 1.15  2005/11/18 10:52:06  jmlarsen
00158  * Split into optimal/sum merge methods
00159  *
00160  * Revision 1.14  2005/11/11 13:18:54  jmlarsen
00161  * Reorganized code, renamed source files
00162  *
00163  */
00164 
00165 #ifdef HAVE_CONFIG_H
00166 #  include <config.h>
00167 #endif
00168 
00169 /*----------------------------------------------------------------------------*/
00175 /*----------------------------------------------------------------------------*/
00179 /*-----------------------------------------------------------------------------
00180                                 Includes
00181  -----------------------------------------------------------------------------*/
00182 
00183 #include <uves_merge.h>
00184 
00185 #include <uves_pfits.h>
00186 #include <uves_utils.h>
00187 #include <uves_utils_wrappers.h>
00188 #include <uves_dump.h>
00189 #include <uves_dfs.h>
00190 #include <uves_error.h>
00191 
00192 #include <cpl.h>
00193 #include <float.h>
00194 #include <string.h>
00195 /*-----------------------------------------------------------------------------
00196                             Functions prototypes
00197  ----------------------------------------------------------------------------*/
00198 
00199 /*-----------------------------------------------------------------------------
00200                             Implementation
00201  ----------------------------------------------------------------------------*/
00202 
00203 /*---------------------------------------------------------------------------*/
00230 /*---------------------------------------------------------------------------*/
00231 
00232 cpl_image *
00233 uves_merge_orders(const cpl_image *spectrum, 
00234                   const cpl_image *spectrum_noise,
00235                   const uves_propertylist *spectrum_header,
00236                   merge_method m_method,
00237                   int n_traces,
00238                   uves_propertylist **merged_header,
00239                   const double delt1, 
00240                   const double delt2,
00241                   enum uves_chip chip,
00242                   cpl_image **merged_noise)
00243 {
00244     cpl_image *merged = NULL;    /* Result */
00245 
00246     const double *spectrum_data_double = NULL;
00247     const float  *spectrum_data_float  = NULL;
00248     const cpl_mask *spectrum_badmap    = NULL;
00249     const cpl_binary *spectrum_bad     = NULL;
00250 
00251     const double *noise_data_double = NULL;
00252     const float *noise_data_float   = NULL;
00253     const cpl_mask *noise_badmap    = NULL;
00254     const cpl_binary *noise_bad     = NULL;
00255     cpl_type type;               /* input/output images type */
00256 
00257     int nbins, ny, norders;          /* Input image size. ny = norders*n_traces */
00258     double wavestep;
00259     int bin_min = 0, bin_max = 0;    /* wavelength of min/max bin in units of 'wavestep' */
00260     int total_bins;
00261     int order, trace;
00262     int spectrum_sx=0;
00263     int spectrum_sy=0;
00264     double delt1_bin=0;
00265     double delt2_bin=0;
00266     char* filename=NULL;
00267 
00268     cpl_vector* image_1d=NULL;
00269     uves_propertylist* hext=NULL;
00270     //double med_noise=0;
00271     passure( spectrum != NULL, " ");
00272     passure( spectrum_noise != NULL, " ");
00273     passure( spectrum_header != NULL, " ");
00274     passure( merged_header != NULL, " ");
00275     passure( merged_noise != NULL, " ");
00276 
00277     assure( m_method == MERGE_OPTIMAL || 
00278             m_method == MERGE_SUM || 
00279             m_method == MERGE_NOAPPEND, 
00280             CPL_ERROR_ILLEGAL_INPUT,
00281             "Unknown merge method: %d", m_method);
00282     
00283     assure( cpl_image_get_type(spectrum) == CPL_TYPE_DOUBLE ||
00284             cpl_image_get_type(spectrum) == CPL_TYPE_FLOAT,
00285             CPL_ERROR_TYPE_MISMATCH,
00286             "Spectrum must have type double or float. It is '%s'",
00287             uves_tostring_cpl_type(cpl_image_get_type(spectrum)));
00288     
00289     assure( cpl_image_get_type(spectrum_noise) == CPL_TYPE_DOUBLE ||
00290             cpl_image_get_type(spectrum_noise) == CPL_TYPE_FLOAT,
00291             CPL_ERROR_TYPE_MISMATCH,
00292             "Spectrum noise must have type double. It is '%s'",
00293             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)));
00294 
00295     assure( cpl_image_get_type(spectrum) ==
00296             cpl_image_get_type(spectrum_noise),
00297             CPL_ERROR_TYPE_MISMATCH,
00298             "Spectrum and spectrum noise must have same type. They are "
00299             "%s and %s, respectively",
00300             uves_tostring_cpl_type(cpl_image_get_type(spectrum)),
00301             uves_tostring_cpl_type(cpl_image_get_type(spectrum_noise)) );
00302 
00303     type = cpl_image_get_type(spectrum);
00304 
00305     /* Read input spectrum geometry */
00306     nbins           = cpl_image_get_size_x(spectrum);
00307     ny              = cpl_image_get_size_y(spectrum);
00308 
00309     assure( cpl_image_get_size_x(spectrum_noise) == nbins &&
00310             cpl_image_get_size_y(spectrum_noise) == ny,
00311             CPL_ERROR_INCOMPATIBLE_INPUT,
00312             "Incompatible spectrum/noise image sizes: %dx%d vs. %" CPL_SIZE_FORMAT "x%" CPL_SIZE_FORMAT "",
00313             nbins, ny,
00314             cpl_image_get_size_x(spectrum_noise),
00315             cpl_image_get_size_y(spectrum_noise) );
00316     
00317     assure( ny % n_traces == 0, CPL_ERROR_INCOMPATIBLE_INPUT,
00318             "Spectrum image height (%d) is not a multiple of "
00319             "the number of traces (%d). Confused, bailing out",
00320             ny, n_traces);
00321 
00322     norders         = ny / n_traces;
00323     
00324     check( wavestep = uves_pfits_get_cdelt1(spectrum_header),
00325        "Error reading bin width");
00326 
00327     /* Get data pointers (for efficiency) */
00328    
00329     if (type == CPL_TYPE_DOUBLE) {
00330         spectrum_data_double   = cpl_image_get_data_double_const(spectrum);
00331     }
00332     else {
00333         spectrum_data_float   = cpl_image_get_data_float_const(spectrum);
00334     }
00335 
00336     spectrum_sx=cpl_image_get_size_x(spectrum);
00337     spectrum_sy=cpl_image_get_size_y(spectrum);
00338 
00339     spectrum_badmap = cpl_image_get_bpm_const(spectrum);
00340     spectrum_bad    = cpl_mask_get_data_const(spectrum_badmap);
00341     
00342     if (type == CPL_TYPE_DOUBLE) {
00343         noise_data_double = cpl_image_get_data_double_const(spectrum_noise);        
00344     }
00345     else {
00346         noise_data_float  = cpl_image_get_data_float_const(spectrum_noise);
00347     }
00348     noise_badmap = cpl_image_get_bpm_const(spectrum_noise);
00349     noise_bad    = cpl_mask_get_data_const(noise_badmap);
00350     uves_msg("delt1=%f delt2=%f",delt1,delt2);
00351     /* Read max/min lambda */
00352     for (order = 1; order <= norders; order++)
00353     {
00354         double wstart, wend;
00355         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00356            "Error reading start wavelength for order #%d", order);
00357 
00358         check( wend = uves_pfits_get_wend(spectrum_header, order),
00359            "Error reading end wavelength for order #%d", order);
00360         
00361         uves_msg_debug("Order #%d: wstart - wend = %f - %f wlu", order, wstart, wend);
00362 
00363     //wstart+=delt1;
00364     //wend-=delt2;
00365 
00366         if (order == 1)
00367         {
00368             bin_min = uves_round_double(wstart/wavestep);
00369             bin_max = uves_round_double(wend  /wavestep);
00370         }
00371         
00372         bin_min = uves_min_int(bin_min, uves_round_double(wstart/wavestep));
00373         bin_max = uves_max_int(bin_max, uves_round_double(wend  /wavestep));
00374     }
00375     total_bins = (bin_max - bin_min) + 1;
00376 
00377     uves_msg_debug("Merging orders into %d bins covering wavelengths %.3f - %.3f wlu", 
00378             total_bins, bin_min * wavestep, bin_max * wavestep);
00379 
00380     /* Initialize spectrum to zero and noise to negative */
00381     if(m_method == MERGE_NOAPPEND) {
00382       merged        = cpl_image_new(total_bins, n_traces*norders, type);
00383       *merged_noise = cpl_image_new(total_bins, n_traces*norders, type);
00384     } else {
00385       merged        = cpl_image_new(total_bins, n_traces, type);
00386       *merged_noise = cpl_image_new(total_bins, n_traces, type);
00387     }
00388     cpl_image_add_scalar(*merged_noise, -1.0);
00389     //cpl_image_power(spectrum_noise,0.5);
00390     //cpl_image_multiply_scalar(spectrum_noise,0.25);
00391     /* Distribute input in output bins */
00392     for (order = 1; order <= norders; order++)
00393     {
00394         double wstart, wend;
00395         int wstart_bin, wend_bin;      /* In 1d space */
00396 
00397 
00398 
00399         check( wstart = uves_pfits_get_wstart(spectrum_header, order),
00400            "Error reading start wavelength for order #%d", order);
00401         
00402         check( wend = uves_pfits_get_wend(spectrum_header, order),
00403            "Error reading end wavelength for order #%d", order);
00404 
00405     //wstart+=delt1;
00406     //wend-=delt2;
00407         
00408         wstart_bin = uves_round_double(wstart/wavestep);
00409         wend_bin   = uves_round_double(wend/wavestep);
00410         delt1_bin  = uves_round_double(delt1/wavestep);
00411         delt2_bin  = uves_round_double(delt2/wavestep);
00412 
00413         
00414     int bin_min_ord = uves_round_double(wstart/wavestep);
00415     int bin_max_ord = uves_round_double(wend  /wavestep);
00416         int nbins_ord = (bin_max_ord - bin_min_ord) + 1;
00417       cpl_image* merged_ord=NULL;
00418       cpl_image * noise_ord=NULL;
00419 
00420     if(m_method == MERGE_NOAPPEND) {
00421       merged_ord = cpl_image_new(nbins_ord, n_traces, type);
00422       noise_ord = cpl_image_new(nbins_ord, n_traces, type);
00423     }
00424 
00425         //if(order>1 && order<norders) {
00426     //  med_noise=cpl_image_get_median_window(spectrum_noise,
00427     //                  1,order,ny,order);
00428     //} else {
00429     //  med_noise=cpl_image_get_median(spectrum_noise);
00430     //}
00431         /* Loop over spatial traces (only 1 trace, unless extraction was 2d) */
00432         for (trace = 1; trace <= n_traces; trace++)
00433         {
00434       int merged_row = 0;
00435       int spectrum_row = (order - 1)*n_traces + trace;
00436       if(m_method == MERGE_NOAPPEND) {
00437         merged_row = (order - 1)*n_traces + trace;
00438       } else {
00439         merged_row = trace;
00440 
00441       }
00442             int rel_bin;                   /* Counting columns in input spectrum */
00443             
00444             for (rel_bin = 1+delt1_bin; 
00445                  (rel_bin <= wend_bin - wstart_bin + 1-delt2_bin) &&
00446                  (rel_bin <(spectrum_sx*spectrum_sy+1-(spectrum_row-1)*nbins));
00447                  rel_bin++)
00448             {
00449                 double flux, noise;
00450                 double current_flux, new_flux;
00451                 double current_noise, new_noise;
00452                 double weight;
00453                 int pis_rejected, noise_rejected;
00454                 
00455                 /* merged_bin = (offset of order)  +  (offset inside order) */
00456                 int merged_bin = (wstart_bin - bin_min) + rel_bin;
00457                 int merged_bin_ord = rel_bin;
00458                 
00459                 passure(1 <= merged_bin && merged_bin <= total_bins,
00460                     "%d %d %d", rel_bin, merged_bin, total_bins);
00461                 
00462                 /* This is slow:
00463                    check( flux  = cpl_image_get(spectrum      , 
00464                           rel_bin, spectrum_row, &pis_rejected);
00465                    noise = cpl_image_get(spectrum_noise, rel_bin, 
00466                     spectrum_row, &noise_rejected),
00467                    "Error reading input spectrum");
00468                 */
00469                 
00470                 if (type == CPL_TYPE_DOUBLE) {
00471                     flux  = spectrum_data_double[(rel_bin-1) + (spectrum_row-1) * nbins];
00472                     noise = noise_data_double   [(rel_bin-1) + (spectrum_row-1) * nbins];
00473 
00474                 }
00475                 else {
00476                     flux  = spectrum_data_float[(rel_bin-1) + (spectrum_row-1) * nbins];
00477                     noise = noise_data_float   [(rel_bin-1) + (spectrum_row-1) * nbins];
00478                 }
00479 
00480                 pis_rejected   = spectrum_bad[(rel_bin-1) + (spectrum_row-1) * nbins];
00481                 noise_rejected = noise_bad   [(rel_bin-1) + (spectrum_row-1) * nbins];
00482                 
00483                 if (!pis_rejected && !noise_rejected)
00484                 {
00485 
00486           if(m_method == MERGE_NOAPPEND) {
00487                     check(( current_flux  = cpl_image_get(merged, 
00488                                                           merged_bin, 
00489                                                           merged_row, 
00490                               &pis_rejected),
00491                 current_noise = cpl_image_get(*merged_noise, 
00492                               merged_bin, 
00493                                                           merged_row, 
00494                               &pis_rejected)),
00495               "Error reading merged spetrum");
00496           } else {
00497                     check(( current_flux  = cpl_image_get(
00498                         merged      , merged_bin, trace, &pis_rejected),
00499                         current_noise = cpl_image_get(
00500                         *merged_noise, merged_bin, trace, &pis_rejected)),
00501                        "Error reading merged spetrum");
00502           }
00503           weight = 1/(noise*noise);
00504                     
00505                     /*
00506                      * Optimal formulas for Variance and Flux are
00507                      *
00508                      *   Vn = ( 1/sigma1^2 + ... +  1/sigmaN^2)^-1
00509                      *   Fn = (f1/sigma1^2 + ... + fN/sigmaN^2) * Vn
00510                      *
00511                      * Update by using these recurrence relations
00512                      *
00513                      *   Fn+1 = (Fn/Vn + fn+1/(sigma_{n+1})^2) * Vn+1  for n > 1
00514                      *   Vn+1 = (Vn^-1 + 1/(sigma_{n+1})^2)^-1  for n > 1
00515                      *
00516                      *
00517                      *  In the case of method = sum,
00518                      *
00519                      *  Vn = sigma1^2 + ... + sigmaN^2
00520                      *  Fn = f1 + ... + fN
00521                      *
00522                      */
00523                     
00524                     if (current_noise > 0)
00525                     {
00526                         if (m_method == MERGE_OPTIMAL)
00527                         {
00528                             new_noise  = 1/(current_noise*current_noise);
00529                             new_noise += weight;
00530                             new_noise  = 1/sqrt(new_noise);
00531                         }
00532                         else if (m_method == MERGE_SUM)
00533                         {
00534                             new_noise = sqrt(current_noise*current_noise
00535                                      + noise*noise);
00536                         }
00537                         else if (m_method == MERGE_NOAPPEND)
00538                         {
00539                             new_noise = current_noise;
00540                         }
00541                         else
00542                         {
00543                             /* Impossible */
00544                             passure( false, "%d", m_method);
00545                         }
00546                     }
00547                     else
00548                     {
00549                         /* First time in this bin */
00550                         new_noise = noise;
00551                     }
00552                     
00553                     if (current_noise > 0)
00554                     {
00555                         if (m_method == MERGE_OPTIMAL)
00556                         {
00557                             new_flux = (current_flux / 
00558                                 (current_noise*current_noise)
00559                                 + flux * weight) * 
00560                             (new_noise*new_noise);
00561                         }
00562                         else if (m_method == MERGE_SUM)
00563                         {
00564                             new_flux = current_flux + flux;
00565                         }
00566                         else if (m_method == MERGE_NOAPPEND)
00567               {
00568                             new_flux = flux;
00569               }
00570                         else
00571                         {
00572                             /* Impossible */
00573                             passure( false, "%d", m_method);
00574                         }
00575                     }
00576                     else
00577                     {
00578                         new_flux = flux;
00579                     }
00580                     
00581           if(m_method == MERGE_NOAPPEND) {
00582 
00583             /*
00584               uves_msg_warning("flux[%d,%d]=%g noise=%g",
00585                        merged_bin,merged_row,
00586                        new_flux,current_noise);
00587             */
00588                     check( cpl_image_set(
00589                      merged, 
00590                                          merged_bin, 
00591                                          merged_row, 
00592                                          new_flux),
00593                        "Error updating merged spectrum");
00594 
00595                     check( cpl_image_set(
00596                      *merged_noise, 
00597                                           merged_bin, 
00598                      merged_row, 
00599                                          new_noise),
00600                        "Error updating weights");
00601 
00602 
00603                     check( cpl_image_set(
00604                      merged_ord, 
00605                                          merged_bin_ord, 
00606                                          trace, 
00607                                          new_flux),
00608                        "Error updating merged spectrum");
00609 
00610                     check( cpl_image_set(
00611                      noise_ord, 
00612                                          merged_bin_ord, 
00613                                          trace, 
00614                                          new_noise),
00615                        "Error updating merged spectrum");
00616 
00617 
00618           } else {
00619                     check( cpl_image_set(
00620                            merged      , merged_bin, trace, new_flux),
00621                        "Error updating merged spectrum");
00622                     check( cpl_image_set(
00623                            *merged_noise, merged_bin, trace, new_noise),
00624                        "Error updating weights");
00625           }
00626 /*            uves_msg("Input flux = %e +- %e ;  
00627             Binned flux changed from %e +- %e to %e +- %e",
00628             flux, noise,
00629             current_flux, current_noise, new_flux, new_noise);*/
00630                     
00631                 } /* If pixel is good ... */
00632 
00633             } /* For each input bin */
00634 
00635         }/* For trace ... */
00636 
00637 
00638     if (merged_header == NULL)
00639         {
00640            uves_free_propertylist(merged_header);
00641            check( *merged_header = uves_initialize_image_header(
00642                      "WAVELENGTH", (n_traces > 1) ? "PIXEL" : " ", "FLUX",
00643                      bin_min_ord * wavestep, 1.0,
00644                      1.0, 1.0,
00645                      wavestep, 1.0),
00646                   "Error initializing merged spectrum header");
00647         }
00648 
00649         if(m_method == MERGE_NOAPPEND) {
00650            filename=uves_sprintf("merged_data_noappend_%s.fits",
00651                            uves_chip_tostring_upper(chip));
00652            image_1d = cpl_vector_wrap(cpl_image_get_size_x(merged_ord),
00653                                       cpl_image_get_data_double(merged_ord));
00654            uves_free_propertylist(&hext);
00655            hext=uves_propertylist_new();
00656            uves_propertylist_append_double(hext,"CRVAL1",wstart-delt1);
00657            uves_propertylist_append_double(hext,"CDELT1",wavestep);
00658            uves_propertylist_append_double(hext,"CRPIX1",0);
00659 
00660            if(order==1) {
00661             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00662                                     CPL_IO_DEFAULT);
00663            } else {
00664             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00665                                     CPL_IO_EXTEND);
00666            }
00667            cpl_vector_unwrap(image_1d);
00668 
00669            image_1d = cpl_vector_wrap(cpl_image_get_size_x(noise_ord),
00670                                       cpl_image_get_data_double(noise_ord));
00671 
00672            uves_free(filename);
00673       
00674            filename=uves_sprintf("merged_sigma_noappend_%s.fits",
00675                                  uves_chip_tostring_upper(chip));
00676            if(order==1) {
00677             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00678                                     CPL_IO_DEFAULT);
00679            } else {
00680             uves_vector_save(image_1d,filename,CPL_BPP_IEEE_FLOAT,hext, 
00681                                     CPL_IO_EXTEND);
00682            }
00683            cpl_vector_unwrap(image_1d);
00684 
00685            uves_free(filename);
00686            uves_free_image(&merged_ord);
00687            uves_free_image(&noise_ord);
00688            uves_free_propertylist(&hext);
00689            uves_free_propertylist(merged_header);
00690         }
00691 
00692     }/* For order ... */
00693     
00694     /* Undefined bins have  (flux, noise) = (0, -1)  (the initial values).
00695      * Set to (flux, noise) = (0, 1)
00696      */
00697 
00698 /* Here commented out piece of code to be used eventually to have
00699    noappend files files as products
00700     if(m_method == MERGE_NOAPPEND) {
00701        cpl_frame* mdata_noappend=NULL;
00702        cpl_frame* msigma_noappend=NULL;
00703        mdata_noappend=cpl_frame_new();
00704        msigma_noappend=cpl_frame_new();
00705        cpl_frame_set_group(mdata_noappend,CPL_FRAME_GROUP_PRODUCT);
00706        cpl_frame_set_type(mdata_noappend,CPL_FRAME_TYPE_IMAGE);
00707        cpl_frame_set_level(mdata_noappend,CPL_FRAME_LEVEL_FINAL);
00708 
00709        tag=uves_sprintf("MERGED_SCI_NOAPPEND_%s",
00710                              uves_chip_tostring_upper(chip));
00711        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00712        cpl_frame_set_tag(mdata_noappend,tag);
00713        cpl_frame_set_filename(mdata_noappend,filename);
00714        uves_free(filename);
00715        uves_free(tag);
00716 
00717        cpl_frame_set_group(msigma_noappend,CPL_FRAME_GROUP_PRODUCT);
00718        cpl_frame_set_type(msigma_noappend,CPL_FRAME_TYPE_IMAGE);
00719        cpl_frame_set_level(msigma_noappend,CPL_FRAME_LEVEL_FINAL);
00720 
00721        tag=uves_sprintf("MERGED_ERR_NOAPPEND_%s",
00722                              uves_chip_tostring_upper(chip));
00723        filename=uves_sprintf("%s_%s.fits",tag,uves_chip_tostring_upper(chip));
00724        cpl_frame_set_tag(msigma_noappend,tag);
00725        cpl_frame_set_filename(msigma_noappend,filename);
00726 
00727        uves_free_frame(&mdata_noappend);
00728        uves_free_frame(&msigma_noappend);
00729        uves_free(filename);
00730        uves_free(tag);
00731 
00732     }
00733 */
00734     check( cpl_image_threshold(*merged_noise, 
00735                    0, DBL_MAX,        /* Outside this interval */
00736                    1, 1),             /* Set to these values   */
00737        "Error setting undefined noise");
00738  
00739     
00740     if (merged_header != NULL)
00741     {
00742         check( *merged_header = uves_initialize_image_header(
00743                "WAVELENGTH [Ang]", (n_traces > 1) ? "PIXEL" : " ", "ADU",
00744                bin_min * wavestep, 1.0,
00745                1.0, 1.0,
00746                wavestep, 1.0),
00747            "Error initializing merged spectrum header");
00748     }
00749  
00750     
00751   cleanup:
00752     return merged;
00753 }
00754 
00755 /*---------------------------------------------------------------------------*/
00765 /*---------------------------------------------------------------------------*/
00766 merge_method
00767 uves_get_merge_method(const cpl_parameterlist *parameters, 
00768                       const char *context, 
00769                       const char *subcontext)
00770 {
00771     const char *mm = "";
00772     merge_method result = 0;
00773     
00774     check( uves_get_parameter(parameters, context, subcontext, "merge", CPL_TYPE_STRING, &mm),
00775        "Could not read parameter");
00776     
00777     if      (strcmp(mm, "optimal") == 0) result = MERGE_OPTIMAL;
00778     else if (strcmp(mm, "sum"    ) == 0) result = MERGE_SUM;
00779     else if (strcmp(mm, "noappend") == 0) result = MERGE_NOAPPEND;
00780     else
00781     {
00782         assure(false, CPL_ERROR_ILLEGAL_INPUT, "No such merging method: '%s'", mm);
00783     }
00784     
00785   cleanup:
00786     return result;
00787 }
00788     
00789 

Generated on 9 Mar 2012 for UVES Pipeline Reference Manual by  doxygen 1.6.1