sinfo_remove_crh_single.c

00001 /*                                                                            *
00002  *   This file is part of the ESO X-shooter Pipeline                          *
00003  *   Copyright (C) 2006 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  * $Author: amodigli $
00022 
00023  * $Date: 2010/12/29 12:29:05 $
00024  * $Revision: 1.4 $
00025  * $Log: sinfo_remove_crh_single.c,v $
00026  * Revision 1.4  2010/12/29 12:29:05  amodigli
00027  * fixed doxygen warning, and bug in kernel filter indexing
00028  *
00029  * Revision 1.3  2009/09/03 15:04:48  kmirny
00030  * replacing deprecated functions
00031  *
00032  * Revision 1.2  2009/02/18 10:33:07  amodigli
00033  * fixed compiler warning
00034  *
00035  * Revision 1.1  2009/01/02 08:27:58  amodigli
00036  * added to repository
00037  *
00038  *
00039  */
00040 
00041 #ifdef HAVE_CONFIG_H
00042 #  include <config.h>
00043 #endif
00044 
00045 /*----------------------------------------------------------------------------*/
00052 /*----------------------------------------------------------------------------*/
00055 /*-----------------------------------------------------------------------------
00056   Includes
00057 -----------------------------------------------------------------------------*/
00058 
00059 #include <math.h>
00060 
00061 
00062 #include <sinfo_error.h>
00063 #include <sinfo_msg.h>
00064 #include <sinfo_utils_wrappers.h>
00065 #include <cpl.h>
00066 #include "sinfo_utilities.h"
00067 /*-----------------------------------------------------------------------------
00068   Functions prototypes
00069  -----------------------------------------------------------------------------*/
00070 cpl_image * sinfo_remove_crh_single( cpl_image * sci_image,
00071                      double crh_frac_max,
00072                      double sigma_lim,
00073                      double f_lim,
00074                      int max_iter,
00075                      double gain,
00076                      double ron);
00077 /*-----------------------------------------------------------------------------
00078   Implementation
00079  -----------------------------------------------------------------------------*/
00080 
00081 /* This should be defined in a more clever way, a parameter for example */
00082 #define MAX_ITERATIONS 6
00083 
00084 
00106 cpl_image * sinfo_remove_crh_single( cpl_image * sci_image,
00107                      double crh_frac_max,
00108                      double sigma_lim,
00109                      double f_lim,
00110                      int max_iter,
00111                      double gain,
00112                      double ron)
00113 {
00114   int i,j,k,l,m;
00115   double  frac = 0. ;
00116   /* Only pointers */
00117 
00118   /* Need to be free */
00119   //xsh_localization_list * loc_list = NULL ;
00120   cpl_image* laplacian_image = NULL;
00121   cpl_image* laplacian_redu_image = NULL;
00122   cpl_image* two_sub_sample = NULL;
00123   cpl_image* sci_median5_image = NULL;
00124   cpl_image* noise_image = NULL;
00125   cpl_image* s_image = NULL;
00126   cpl_image* s_median_image = NULL;
00127   cpl_image* s2_image = NULL;
00128   cpl_image* sci_median3_image = NULL;
00129   cpl_image* sci_median3_7_image = NULL;
00130   cpl_image* f_image = NULL;
00131   cpl_image* r_image = NULL;
00132   int two_sub_sample_nx = 0;
00133   int two_sub_sample_ny = 0;
00134   /* Only pointers */
00135   float* sci_data = NULL;
00136   float* two_sub_sample_data = NULL;
00137   float* laplacian_data = NULL;
00138   float* laplacian_redu_data = NULL;
00139   float* sci_median5_data = NULL;
00140   float* sci_median3_data = NULL;
00141   float* sci_median3_7_data = NULL;
00142   float* noise_data = NULL;
00143   float* s_data = NULL;
00144   float* s_median_data = NULL;
00145   float* s2_data = NULL;
00146   float* f_data = NULL;
00147   float* r_data = NULL;
00148   /* Need to be free */
00149   float* cosmic_data = NULL;
00150 
00151   cpl_matrix* laplacian_kernel = NULL;
00152   cpl_matrix* median3_kernel = NULL;
00153   cpl_matrix* median5_kernel = NULL;
00154   cpl_matrix* median7_kernel = NULL;
00155   int new_crh =1, nb_crh = 0;
00156   int nbiter = 1 ;
00157   cpl_vector* median = NULL;
00158   //const char * tag = NULL ;
00159   int nx=0;
00160   int ny=0;
00161   cpl_image* res_image=NULL;
00162 
00163   /* Check parameters */
00164   cknull( sci_image,"null input image" ) ; ;
00165 
00166   sinfo_msg( "Entering sinfo_remove_crh_single");
00167   sinfo_msg( "  Params: frac_max %.1f, sigma_lim %.2f f_lim %.2f, iter %d",
00168        crh_frac_max, sigma_lim, f_lim, max_iter);
00169 
00170   /* Preparing different kernels */
00171   nx=cpl_image_get_size_x(sci_image);
00172   ny=cpl_image_get_size_y(sci_image);
00173 
00174   /* Laplacian */
00175   check_nomsg( laplacian_kernel = cpl_matrix_new(3,3));
00176   cpl_matrix_set( laplacian_kernel,0,0,0.0);
00177   cpl_matrix_set( laplacian_kernel,0,1,-1.0);
00178   cpl_matrix_set( laplacian_kernel,0,2,0.0);
00179   cpl_matrix_set( laplacian_kernel,1,0,-1.0);
00180   cpl_matrix_set( laplacian_kernel,1,1,4.0);
00181   cpl_matrix_set( laplacian_kernel,1,2,-1.0);
00182   cpl_matrix_set( laplacian_kernel,2,0,0.0);
00183   cpl_matrix_set( laplacian_kernel,2,1,-1.0);
00184   cpl_matrix_set( laplacian_kernel,2,2,0.0);
00185   cpl_matrix_divide_scalar( laplacian_kernel, 4.0);
00186 /*
00187   cpl_matrix_set( laplacian_kernel,0,0,-1.0);
00188   cpl_matrix_set( laplacian_kernel,0,1,-1.0);
00189   cpl_matrix_set( laplacian_kernel,0,2,-1.0);
00190   cpl_matrix_set( laplacian_kernel,1,0,-1.0);
00191   cpl_matrix_set( laplacian_kernel,1,1,8.0);
00192   cpl_matrix_set( laplacian_kernel,1,2,-1.0);
00193   cpl_matrix_set( laplacian_kernel,2,0,-1.0);
00194   cpl_matrix_set( laplacian_kernel,2,1,-1.0);
00195   cpl_matrix_set( laplacian_kernel,2,2,-1.0);
00196   cpl_matrix_divide_scalar( laplacian_kernel, 8.0);
00197 */
00198   /* Median 3x3*/
00199   check_nomsg( median3_kernel = cpl_matrix_new(3,3));
00200   for(j=0; j< 3; j++){
00201     for(i=0; i< 3; i++){
00202       cpl_matrix_set( median3_kernel, i,j,1.0);
00203     }
00204   }
00205 
00206   /* Median 5x5 */
00207   check_nomsg( median5_kernel = cpl_matrix_new(5,5));
00208   for(j=0; j< 5; j++){
00209     for(i=0; i< 5; i++){
00210       cpl_matrix_set( median5_kernel, i,j,1.0);
00211     }
00212   }
00213 
00214   /* Median 7x7 */
00215   check_nomsg( median7_kernel = cpl_matrix_new(7,7));
00216   for(j=0; j< 7; j++){
00217     for(i=0; i< 7; i++){
00218       cpl_matrix_set( median7_kernel, i,j,1.0);
00219     }
00220   }
00221 
00222   check_nomsg (res_image = cpl_image_duplicate( sci_image));
00223 
00224   /* Allocate images and pointers */
00225   check_nomsg (sci_data = cpl_image_get_data_float( res_image));
00226 
00227   two_sub_sample_nx = nx*2;
00228   two_sub_sample_ny = ny*2;
00229   check_nomsg( two_sub_sample = cpl_image_new( two_sub_sample_nx,
00230     two_sub_sample_ny, CPL_TYPE_FLOAT));
00231   check_nomsg(two_sub_sample_data = cpl_image_get_data_float( two_sub_sample));
00232   check_nomsg( laplacian_redu_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00233   check_nomsg(laplacian_redu_data = cpl_image_get_data_float(
00234     laplacian_redu_image));
00235   check_nomsg( noise_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00236   check_nomsg( noise_data = cpl_image_get_data_float( noise_image));
00237   check_nomsg( s_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00238   check_nomsg( s_data = cpl_image_get_data_float( s_image));
00239   check_nomsg( s2_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00240   check_nomsg( s2_data = cpl_image_get_data_float( s2_image));
00241   check_nomsg( f_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00242   check_nomsg( f_data = cpl_image_get_data_float( f_image));
00243   check_nomsg( r_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
00244   check_nomsg( r_data = cpl_image_get_data_float( r_image));
00245   cosmic_data=cpl_calloc(nx*ny, sizeof(float));
00246 
00247   /* LGG - Added limit on frac_max AND limit on nb iterations */
00248   while( new_crh > 0 && frac < crh_frac_max && nbiter <= max_iter ){
00249     sinfo_msg("Iteration %d",nbiter );
00250     /* Create a 2n x 2n images like this
00251         | 1 | 2 |  =>  | 1 | 1 | 2 | 2 |
00252         | 3 | 4 |      | 1 | 1 | 2 | 2 |
00253                        | 3 | 3 | 4 | 4 |
00254                        | 3 | 3 | 4 | 4 | */
00255     sinfo_msg_debug("Create a 2n images");
00256     for( j=0; j< ny; j++){
00257       for( i=0; i< nx; i++){
00258         float val = sci_data[i+j*nx];
00259 
00260     if ( val < 0. ) val = 0. ;
00261         two_sub_sample_data[i*2+j*2*two_sub_sample_nx] = val;
00262         two_sub_sample_data[i*2+1+j*2*two_sub_sample_nx] = val;
00263         two_sub_sample_data[i*2+(j*2+1)*two_sub_sample_nx] = val;
00264         two_sub_sample_data[i*2+1+(j*2+1)*two_sub_sample_nx] = val;
00265       }
00266     }
00267     sinfo_msg_debug("Doing laplacian convolution");
00268     /* Doing the laplacian convolution
00269         0  -1   0
00270        -1   4  -1
00271         0  -1   0 */
00272     laplacian_image = sinfo_image_filter_linear( two_sub_sample,
00273       laplacian_kernel);
00274 
00275     /* multiply by two to normalize correctly the laplacian [RD5]
00276        and filter negative values */
00277     sinfo_msg_debug("Normalize laplacian");
00278     check_nomsg (laplacian_data = cpl_image_get_data_float( laplacian_image));
00279     for ( i=0; i< two_sub_sample_nx*two_sub_sample_ny; i++){
00280       if (laplacian_data[i] > 0.0){
00281         laplacian_data[i] = 2.0 * laplacian_data[i];
00282       }
00283       else{
00284         laplacian_data[i] = 0.0;
00285       }
00286     }
00287     sinfo_msg_debug("Save Lpositive");
00288     cpl_image_save(laplacian_image, "Lpositive.fits", CPL_BPP_IEEE_FLOAT, NULL,
00289       CPL_IO_DEFAULT);
00290 
00291     /* resample to the original size
00292        | 1 | 1 | 2 | 2 |    | 1 | 2 |
00293        | 1 | 1 | 2 | 2 |    | 3 | 4 |
00294        | 3 | 3 | 4 | 4 | =>
00295        | 3 | 3 | 4 | 4 |               */
00296 
00297     sinfo_msg_debug("Resample to the original size");
00298 
00299     for( j=0; j< ny; j++){
00300       for( i=0; i< nx; i++){
00301         laplacian_redu_data[i+j*nx] =
00302           (laplacian_data[i*2+j*2*two_sub_sample_nx]+
00303            laplacian_data[i*2+1+j*2*two_sub_sample_nx]+
00304            laplacian_data[i*2+(j*2+1)*two_sub_sample_nx]+
00305            laplacian_data[i*2+1+(j*2+1)*two_sub_sample_nx])/4.0;
00306       }
00307     }
00308 
00309     cpl_image_save(laplacian_redu_image, "Lplus.fits", CPL_BPP_IEEE_FLOAT,
00310       NULL, CPL_IO_DEFAULT);
00311 
00312     sinfo_msg_debug("Apply median filter");
00313     /* Apply 5x5 median filter on data */
00314     check_nomsg( sci_median5_image = sinfo_image_filter_median( sci_image,
00315       median5_kernel));
00316     check_nomsg (sci_median5_data = cpl_image_get_data_float( sci_median5_image));
00317 
00318     sinfo_msg_debug("Compute noise");
00319     /* computes the noise image */
00320     for( i=0; i< nx*ny; i++){
00321       noise_data[i] = sqrt(sci_median5_data[i]*gain+
00322         ron*ron)/ gain;
00323     }
00324 
00325     sinfo_msg_debug("Compute S");
00326     /* compute S image */
00327     for( i=0; i< nx*ny; i++){
00328       s_data[i] = laplacian_redu_data[i] / (2.0*noise_data[i]);
00329     }
00330 
00331     sinfo_msg_debug("Compute S median");
00332     /* compute S median image */
00333     check_nomsg( s_median_image = sinfo_image_filter_median( s_image,
00334       median5_kernel));
00335     check_nomsg( s_median_data = cpl_image_get_data_float( s_median_image));
00336 
00337     sinfo_msg_debug("Compute s2");
00338     /* compute s2 */
00339     for( i=0; i< nx*ny; i++){
00340       s2_data[i] = s_data[i] -s_median_data[i];
00341     }
00342 
00343        cpl_image_save( s2_image, "S2.fits", CPL_BPP_IEEE_FLOAT, NULL,
00344      CPL_IO_DEFAULT);
00345 
00346     sinfo_msg_debug("Apply 3x3 filter");
00347     /* Apply 3x3 median filter on data */
00348     check_nomsg( sci_median3_image = sinfo_image_filter_median( sci_image,
00349       median3_kernel));
00350 
00351     sinfo_msg_debug("Apply 7x7 filter");
00352     /* Apply 7x7 median filter */
00353     check_nomsg( sci_median3_7_image = sinfo_image_filter_median( sci_median3_image,
00354       median7_kernel));
00355     sinfo_msg_debug("Apply 7x7 filter ok");
00356     check_nomsg ( sci_median3_data = cpl_image_get_data_float( sci_median3_image));
00357     check_nomsg ( sci_median3_7_data = cpl_image_get_data_float(
00358       sci_median3_7_image));
00359 
00360     sinfo_msg_debug("Compute F");
00361     /* compute F */
00362     for( i=0; i< nx*ny; i++){
00363       f_data[i] = sci_median3_data[i] -sci_median3_7_data[i];
00364       if (f_data[i] < 0.01){
00365         f_data[i] = 0.01;
00366       }
00367     }
00368     cpl_image_save( f_image, "F.fits", CPL_BPP_IEEE_FLOAT, NULL,
00369       CPL_IO_DEFAULT);
00370 
00371     sinfo_msg_debug("Compute R");
00372     /* compute R */
00373     for( i=0; i< nx*ny; i++){
00374       r_data[i] = laplacian_redu_data[i]/f_data[i];
00375     }
00376 
00377     cpl_image_save( r_image, "R.fits", CPL_BPP_IEEE_FLOAT, NULL,
00378       CPL_IO_DEFAULT);
00379 
00380     /* Search for cosmics */
00381 
00382     sinfo_msg_debug("Search for cosmic");
00383     new_crh = 0;
00384     median = cpl_vector_new(24);
00385 
00386     for( j=1; j< ny-1; j++){
00387       double *data = NULL;
00388       cpl_vector* med_vect = NULL;
00389 
00390       for( i=1; i< nx-1; i++){
00391         if ( (s2_data[i+j*nx] >= sigma_lim) &&
00392           (r_data[i+j*nx] >= f_lim)){
00393           int li,lj,ui,uj;
00394           cosmic_data[i+j*nx] = 1.0;
00395           new_crh++;
00396           li = i-2;
00397           lj = j-2;
00398           ui = i+2;
00399           uj = j+2;
00400           m = 0;
00401           if (li < 0) li = 0;
00402           if (ui >= nx) ui = nx-1;
00403           if (lj < 0) lj = 0;
00404           if (uj >= ny) uj = ny-1;
00405           for( k=lj; k <= uj; k++){
00406             for( l=li; l <= ui; l++){
00407               //sinfo_msg("REGDEBUG k %d l %d m %d", k, l, m);
00408               if ( k < j){
00409                 cpl_vector_set(median, m, sci_data[l+k*nx]);
00410                 m++;
00411               }
00412               else if ( (k == j) && ( l < i)){
00413                  cpl_vector_set(median, m, sci_data[l+k*nx]);
00414                 m++;
00415               }
00416               else if ( l!=i && k!=j && (s2_data[l+k*nx] < sigma_lim)
00417                 && (r_data[l+k*nx] < f_lim)){
00418                 cpl_vector_set(median, m, sci_data[l+k*nx]);
00419                 m++;
00420               }
00421             }
00422           }
00423           check_nomsg( data = cpl_vector_get_data( median));
00424           sinfo_msg_debug("REGDEBUG i %d j %d m %d", i, j ,m);
00425           check_nomsg( med_vect = cpl_vector_wrap( m, data));
00426           check_nomsg( sci_data[i+j*nx] = cpl_vector_get_median( med_vect));
00427           cpl_vector_unwrap( med_vect);
00428         }
00429       }
00430     }
00431     sinfoni_free_vector( &median ) ;
00432     nb_crh += new_crh;
00433     frac = (double)nb_crh/(double)(nx*ny) ;
00434     sinfo_msg("   new cosmics %d, total %d, frac %.4f [%d pixels]",new_crh,nb_crh,
00435         frac, nx*ny);
00436     nbiter++;
00437     sinfo_free_image( &laplacian_image);
00438     sinfo_free_image( &sci_median3_7_image ) ;
00439     sinfo_free_image( &sci_median3_image ) ;
00440     sinfo_free_image( &s_median_image ) ;
00441     sinfo_free_image( &sci_median5_image ) ;
00442   }
00443   {
00444     FILE *debug = NULL;
00445 
00446     debug = fopen("cosmic.log","w");
00447 
00448     for( j=0; j< ny; j++){
00449       for( i=0; i< nx; i++){
00450         if ( cosmic_data[i+j*nx] == 1.0){
00451           fprintf(debug,"%.1f %.1f\n",i+1.0,j+1.0);
00452         }
00453       }
00454     }
00455     fclose(debug);
00456   }
00457 
00458   //check_nomsg( res_frame = cpl_frame_duplicate( sci_frame ) ) ;
00459   //sinfo_msg( "Saving Result Frame '%s'", res_name ) ;
00460   //check_nomsg( add_qc_crh( sci_pre, nb_crh, 1, instrument ) ) ;
00461   //check_nomsg( res_frame = xsh_pre_save( sci_pre, res_name, 1 ) ) ;
00462   //tag = cpl_frame_get_tag( in_sci_frame ) ;
00463   //check_nomsg( cpl_frame_set_tag( res_frame, tag ) ) ;
00464 
00465   cleanup:
00466   //xsh_pre_free( &sci_pre);
00467   //xsh_localization_list_free( &loc_list ) ;
00468 
00469     /* free kernel */
00470     sinfoni_free_matrix( &laplacian_kernel);
00471     sinfoni_free_matrix( &median3_kernel);
00472     sinfoni_free_matrix( &median5_kernel);
00473     sinfoni_free_matrix( &median7_kernel);
00474     /* free images */
00475     sinfo_free_image( &laplacian_image);
00476     sinfo_free_image( &laplacian_redu_image);
00477     sinfo_free_image( &two_sub_sample);
00478     sinfo_free_image( &sci_median5_image);
00479     sinfo_free_image( &noise_image);
00480     sinfo_free_image( &s_image);
00481     sinfo_free_image( &s_median_image);
00482     sinfo_free_image( &s2_image);
00483     sinfo_free_image( &sci_median3_image);
00484     sinfo_free_image( &sci_median3_7_image);
00485     sinfo_free_image( &f_image);
00486     sinfo_free_image( &r_image);
00487     /* free vector */
00488     sinfoni_free_vector( &median);
00489     /* free tab */
00490     if(cosmic_data!=NULL) cpl_free( cosmic_data);
00491     return res_image;
00492 }

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