sinfo_utl_cube_combine.c

00001 /* $Id: sinfo_utl_cube_combine.c,v 1.19 2009/02/23 09:03:36 amodigli Exp $
00002  *
00003  * This file is part of the IIINSTRUMENT Pipeline
00004  * Copyright (C) 2002,2003 European Southern Observatory
00005  *
00006  * This program is free software; you can redistribute it and/or modify
00007  * it under the terms of the GNU General Public License as published by
00008  * the Free Software Foundation; either version 2 of the License, or
00009  * (at your option) any later version.
00010  *
00011  * This program is distributed in the hope that it will be useful,
00012  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00013  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00014  * GNU General Public License for more details.
00015  *
00016  * You should have received a copy of the GNU General Public License
00017  * along with this program; if not, write to the Free Software
00018  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
00019  */
00020 
00021 /*
00022  * $Author: amodigli $
00023  * $Date: 2009/02/23 09:03:36 $
00024  * $Revision: 1.19 $
00025  * $Name: sinfo-2_2_5 $
00026  */
00027 
00028 #ifdef HAVE_CONFIG_H
00029 #  include <config.h>
00030 #endif
00031 
00032 /*----------------------------------------------------------------------------
00033                                 Includes
00034  ---------------------------------------------------------------------------*/
00035 
00036 #include "sinfo_utl_cube_combine.h"
00037 #include "sinfo_utilities.h"
00038 #include "sinfo_utilities_scired.h"
00039 #include <stdio.h>
00040 #include "sinfo_key_names.h"
00041 #include "sinfo_error.h"
00042 #include "sinfo_utils_wrappers.h"
00043 #include "sinfo_pro_save.h"
00044 /*-----------------------------------------------------------------------------
00045                             Functions prototypes
00046  ----------------------------------------------------------------------------*/
00047 
00048 
00049 /*-----------------------------------------------------------------------------
00050                             Static variables
00051  ----------------------------------------------------------------------------*/
00052 
00053 
00054 /*-----------------------------------------------------------------------------
00055                                 Functions code
00056  ----------------------------------------------------------------------------*/
00066 /*---------------------------------------------------------------------------*/
00073 /*---------------------------------------------------------------------------*/
00074 int sinfo_utl_cube_combine(
00075         cpl_parameterlist   *   parlist, 
00076         cpl_frameset        *   framelist)
00077 {
00078     cpl_parameter       *   param=NULL ;
00079     const char                *   name_o=NULL ;
00080     const char                *   name_i=NULL ;
00081     const char                *   name_m=NULL ;
00082    
00083     cpl_propertylist    *   plist=NULL ;
00084     cpl_image           *   image=NULL ;
00085     cpl_frame           *   product_frame=NULL;
00086     cpl_frame           *   prod_frm=NULL;
00087     cpl_frame           *   frame=NULL;
00088   
00089     int z=0;
00090     int z_min=0;
00091     int z_max=0;
00092     int z_siz=0;
00093     int z_stp=100;
00094     int xsize=0;
00095     int ysize=0;
00096     int scales_sky=0;
00097 
00098     int i=0;
00099     int j=0;
00100     int n=0;
00101 
00102     int size_x=0;
00103     int size_y=0;
00104     cpl_image* j_img=NULL;
00105     cpl_image* m_img=NULL;
00106  
00107     cpl_imagelist ** cube_object=NULL;
00108     cpl_imagelist * cube_jitter=NULL;
00109     cpl_imagelist * cube_mask=NULL;
00110  
00111     const char**    files=NULL;
00112     int nframes=0;
00113 
00114     double * times=NULL;
00115     float * offsetx=NULL;
00116     float * offsety=NULL;
00117     float  ref_offx=0;
00118     float  ref_offy=0;
00119     float tmpoffx=0;
00120     float tmpoffy=0;
00121     double kappa=2;
00122     int ks_clip=0;
00123     int min_size_x=9999;
00124     int min_size_y=9999;
00125     const char* name=NULL;
00126 
00127  
00128     FILE* file_list=NULL;
00129     int cnt=0;
00130     int onp=0;
00131   
00132     /* HOW TO RETRIEVE INPUT PARAMETERS */
00133     /* --stropt */
00134     check_nomsg(param = cpl_parameterlist_find(parlist, 
00135                         "sinfoni.sinfo_utl_cube_combine.ks_clip"));
00136     check_nomsg(ks_clip = cpl_parameter_get_bool(param));
00137 
00138     check_nomsg(param = cpl_parameterlist_find(parlist, 
00139                         "sinfoni.sinfo_utl_cube_combine.scale_sky"));
00140     check_nomsg(scales_sky = cpl_parameter_get_bool(param));
00141 
00142 
00143     check_nomsg(param = cpl_parameterlist_find(parlist, 
00144                         "sinfoni.sinfo_utl_cube_combine.kappa"));
00145     check_nomsg(kappa = cpl_parameter_get_double(param));
00146 
00147     check_nomsg(param = cpl_parameterlist_find(parlist, 
00148                         "sinfoni.sinfo_utl_cube_combine.name_i"));
00149     check_nomsg(name_i = cpl_parameter_get_string(param));
00150 
00151     check_nomsg(param = cpl_parameterlist_find(parlist, 
00152                         "sinfoni.sinfo_utl_cube_combine.name_o"));
00153     check_nomsg(name_o = cpl_parameter_get_string(param));
00154 
00155 
00156     /* --doubleopt */
00157     check_nomsg(param = cpl_parameterlist_find(parlist,
00158                         "sinfoni.sinfo_utl_cube_combine.xsize"));
00159     check_nomsg(xsize = cpl_parameter_get_int(param));
00160 
00161     check_nomsg(param = cpl_parameterlist_find(parlist,
00162                         "sinfoni.sinfo_utl_cube_combine.ysize"));
00163     check_nomsg(ysize = cpl_parameter_get_int(param));
00164 
00165   
00166   /* Identify the RAW and CALIB frames in the input frameset */
00167     check(sinfo_dfs_set_groups(framelist),
00168          "Cannot identify RAW and CALIB frames") ;
00169  
00170 
00171     /* HOW TO ACCESS INPUT DATA */
00172     n=cpl_frameset_get_size(framelist);
00173     if(n<1) {
00174       sinfo_msg_error("Empty input frame list!");
00175       goto cleanup ;
00176     }
00177     for (i=0;i<n;i++) {
00178        frame=cpl_frameset_get_frame(framelist,i);
00179        cpl_frame_set_group(frame,CPL_FRAME_GROUP_RAW);
00180     }
00181 
00182    
00183 
00184     /* Now performing the data reduction */
00185     /* Let's generate one image for the example */
00186     
00187     if ( NULL == (file_list = fopen (name_i, "r" ) ) )
00188     {      
00189       sinfo_msg_error("cannot open %s\n", name_i) ;
00190       goto cleanup ;
00191     }
00192  
00193     cnt = 0 ;
00194     while ( fscanf( file_list, "%f %f",&tmpoffx, &tmpoffy) != EOF )
00195     {
00196       cnt ++ ;
00197     }
00198     fclose(file_list);
00199    
00200     nframes= cnt ;
00201     cknull(times = (double*) cpl_calloc (nframes, sizeof (double)), 
00202            " could not allocate memory!") ;
00203  
00204     cknull(offsetx = (float*) cpl_calloc (nframes, sizeof(float)),
00205            " could not allocate memory!") ;
00206 
00207     cknull(offsety = (float*) cpl_calloc (nframes, sizeof(float)),
00208            " could not allocate memory!") ;
00209   
00210     files = (const char**) cpl_calloc(MAX_NAME_SIZE,sizeof(const char*));
00211     if ( NULL == (file_list = fopen (name_i, "r" ) ) )
00212     {
00213       sinfo_msg_error("cannot open %s\n", name_i) ;
00214       return -1 ;
00215     }
00216 
00217 
00218     cnt=0;   
00219     while ( fscanf( file_list, "%f %f",&tmpoffx,&tmpoffy ) != EOF ) {
00220       frame=cpl_frameset_get_frame(framelist,cnt);
00221       files[cnt]= cpl_frame_get_filename(frame);
00222       times[cnt]=sinfo_pfits_get_exptime(files[cnt]);
00223       offsetx[cnt]=tmpoffx;
00224       offsety[cnt]=tmpoffy;
00225       plist=cpl_propertylist_load(files[cnt],0);
00226       size_x=sinfo_pfits_get_naxis1(plist);
00227       size_y=sinfo_pfits_get_naxis2(plist);
00228       sinfo_free_propertylist(&plist);
00229       if(size_x < min_size_x) min_size_x=size_x;
00230       if(size_y < min_size_y) min_size_y=size_y;
00231       cnt ++ ;
00232     }
00233     sinfo_msg("Min input cube size x=%d y=%d",min_size_x,min_size_y);
00234  
00235     nframes=cnt;
00236     fclose(file_list);
00237  
00238     ck0(sinfo_auto_size_cube(offsetx,offsety,nframes,
00239                               &ref_offx,&ref_offy,&size_x,&size_y),
00240          "Error resizing cube");
00241     sinfo_msg("output ima size=%dx%d",size_x,size_y); 
00242     cknull(cube_object = cpl_calloc(nframes,sizeof(cpl_imagelist*)),
00243        "could not allocate memory") ;
00244  
00245     for (i=0;i<nframes;i++) {
00246       frame=cpl_frameset_get_frame(framelist,i);
00247       name=cpl_frame_get_filename(frame);
00248       check_nomsg(cube_object[i]=cpl_imagelist_load(name,CPL_TYPE_FLOAT,0));
00249       ck0(sinfo_new_assign_offset2(i,name,offsetx,offsety,
00250                                   ref_offx,ref_offy),
00251                                   "Error assigning offsets");
00252     }
00253     onp = cpl_imagelist_get_size(cube_object[0]);
00254 
00255 
00256     check(cube_jitter = cpl_imagelist_new(),"allocating new data cube object");
00257     check(cube_mask = cpl_imagelist_new(),"allocating new data cube mask");
00258 
00259     check(plist=cpl_propertylist_load(files[0],0),
00260       "Cannot read the FITS header") ;
00261 
00262    if(scales_sky == 1) {
00263       sinfo_msg("Subtract spatial sinfo_median to each cube plane");
00264       for(n=0;n<nframes;n++) {
00265     sinfo_msg("process cube %d\n",n);
00266     sinfo_new_sinfoni_correct_median_it(&(cube_object[n]));
00267       }
00268     }
00269 
00270    for(z=0;z<onp;z+=z_stp) {
00271      z_siz=(z_stp < (onp-z)) ? z_stp : (onp-z);
00272      z_min=z;
00273      z_max=z_min+z_siz;
00274      sinfo_msg("Coadding cubes: range [%4.4d,%4.4d) of 0-%d\n",
00275            z_min,z_max,onp);
00276 
00277      for(j=z_min;j<z_max;j++) {
00278 
00279        check_nomsg(j_img=cpl_image_new(size_x,size_y,CPL_TYPE_FLOAT));
00280        check_nomsg(cpl_imagelist_set(cube_jitter,j_img,j));
00281        check_nomsg(m_img = cpl_image_new(size_x,size_y,CPL_TYPE_FLOAT));
00282        check_nomsg(cpl_imagelist_set(cube_mask,m_img,j));
00283      }
00284      if(ks_clip == 1){
00285        sinfo_new_combine_jittered_cubes_thomas_range(cube_object,
00286                              cube_jitter,
00287                              cube_mask,
00288                              nframes,
00289                              offsetx,offsety,
00290                              times,
00291                              (char*) "tanh",
00292                              z_min,
00293                              z_max,
00294                              kappa);
00295      } else {
00296        sinfo_new_combine_jittered_cubes_range(cube_object, 
00297                           cube_jitter,
00298                           cube_mask,
00299                           nframes,
00300                           offsetx,
00301                           offsety,
00302                           times,
00303                           (char*) "tanh",
00304                           z_min,
00305                           z_max) ;
00306      }
00307       
00308    }
00309    sinfo_new_convert_0_to_ZERO_for_cubes(cube_jitter) ; 
00310  
00311     name_m="out_cube_mask.fits";
00312      /* HOW TO SAVE A PRODUCT ON DISK  */
00313 
00314     /* Create product frame */
00315     check_nomsg(product_frame = cpl_frame_new());
00316     check_nomsg(cpl_frame_set_filename(product_frame, name_o)) ;
00317     check_nomsg(cpl_frame_set_tag(product_frame, SI_UTL_CUBE_COMBINE_PROCUBE));
00318     check_nomsg(cpl_frame_set_type(product_frame, CPL_FRAME_TYPE_IMAGE)) ;
00319     check_nomsg(cpl_frame_set_group(product_frame, CPL_FRAME_GROUP_PRODUCT)) ;
00320     check_nomsg(cpl_frame_set_level(product_frame, CPL_FRAME_LEVEL_FINAL)) ;
00321       
00322     /* Add DataFlow keywords */
00323 #if defined CPL_VERSION_CODE && CPL_VERSION_CODE >= CPL_VERSION(4, 8, 0)  
00324     check(cpl_dfs_setup_product_header(plist, product_frame, 
00325                                        framelist, parlist,
00326                                        "sinfo_utl_cube_combine", 
00327                                        "SINFONI", KEY_VALUE_HPRO_DID,NULL),
00328       "Problem in the product DFS-compliance") ;
00329 #else
00330     check(cpl_dfs_setup_product_header(plist, product_frame, 
00331                                        framelist, parlist,
00332                                        "sinfo_utl_cube_combine",
00333                                        "SINFONI", KEY_VALUE_HPRO_DID),
00334       "Problem in the product DFS-compliance") ;
00335 #endif    
00336     check(cpl_imagelist_save(cube_jitter, name_o, CPL_BPP_IEEE_FLOAT, plist,
00337                  CPL_IO_DEFAULT),"Could not save product");
00338     check_nomsg(cpl_frameset_insert(framelist, product_frame));
00339     
00340    
00341     check_nomsg(prod_frm = cpl_frame_new());
00342     check_nomsg(cpl_frame_set_filename(prod_frm, name_m)) ;
00343     check_nomsg(cpl_frame_set_tag(prod_frm, SI_UTL_CUBE_COMBINE_PROMASK)) ;
00344     check_nomsg(cpl_frame_set_type(prod_frm, CPL_FRAME_TYPE_IMAGE)) ;
00345     check_nomsg(cpl_frame_set_group(prod_frm, CPL_FRAME_GROUP_PRODUCT)) ;
00346     check_nomsg(cpl_frame_set_level(prod_frm, CPL_FRAME_LEVEL_FINAL)) ;
00347 
00348     check(cpl_imagelist_save(cube_mask, name_m, CPL_BPP_IEEE_FLOAT, plist,
00349                  CPL_IO_DEFAULT),"Could not save product");
00350     check_nomsg(cpl_frameset_insert(framelist, prod_frm));
00351     
00352  cleanup:
00353     sinfo_free_imagelist(&cube_jitter) ;
00354     sinfo_free_image(&image) ;
00355     sinfo_free_imagelist(&cube_mask) ;
00356 
00357 
00358     if(cube_object != NULL) {
00359       for (i=0;i< nframes;i++){
00360     sinfo_free_imagelist(&(cube_object[i]));      
00361       }
00362       sinfo_free_array_imagelist(&cube_object);
00363     }
00364     sinfo_free_propertylist(&plist);
00365     if(files != NULL) {
00366       cpl_free(files);
00367       files=NULL;
00368     }
00369     sinfo_free_double(&times);
00370     sinfo_free_float(&offsetx);
00371     sinfo_free_float(&offsety);
00372  
00373     /* Return */
00374     if (cpl_error_get_code()) {
00375         return -1 ;
00376     }
00377     else { 
00378         return 0 ;
00379     }
00380 }

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