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/* *
* This file is part of the ESO X-shooter Pipeline *
* Copyright (C) 2006 European Southern Observatory *
* *
* This library is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the Free Software *
* Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02111-1307 USA *
* */
/*
* $Author: amodigli $
* $Date: 2012-03-03 10:18:26 $
* $Revision: 1.5 $
*
*/
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
/**@{*/
/*----------------------------------------------------------------------------*/
/**
* @defgroup sinfo_remove_crh_single Remove Cosmic Rays single (sinfo_remove_crh_single)
* @ingroup drl_functions
*
* Suppress Cosmic Rays by analysing on files
*/
/*----------------------------------------------------------------------------*/
/*-----------------------------------------------------------------------------
Includes
-----------------------------------------------------------------------------*/
#include <math.h>
#include <sinfo_error.h>
#include <sinfo_msg.h>
#include <sinfo_utils_wrappers.h>
#include <cpl.h>
#include "sinfo_utilities.h"
/*-----------------------------------------------------------------------------
Functions prototypes
-----------------------------------------------------------------------------*/
cpl_image * sinfo_remove_crh_single( cpl_image * sci_image,
double crh_frac_max,
double sigma_lim,
double f_lim,
int max_iter,
double gain,
double ron);
/*-----------------------------------------------------------------------------
Implementation
-----------------------------------------------------------------------------*/
/* This should be defined in a more clever way, a parameter for example */
#define MAX_ITERATIONS 6
/**
* Remove cosmic rays from a single frame.
*
* @param[in] sci_image
* The science image
* @param[in] crh_frac_max
* The maximum fraction of pixel over total detector pixels flagged as CRHs
* @param[in] sigma_lim
* Poisson fluctuation threshold to flag CRHs
* @param[in] f_lim
* Minimum contrast between the Laplacian image and the fine structure
* image that a point must have to be flagged as CRH.
* @param[in] max_iter
* Maximum number of iterations performed to flag CRHs
* @param[in] gain
* Detector's gain
* @param[in] ron
* Detector's read out noise value
*
* @return The science image after removal of Cosmics
*/
cpl_image * sinfo_remove_crh_single( cpl_image * sci_image,
double crh_frac_max,
double sigma_lim,
double f_lim,
int max_iter,
double gain,
double ron)
{
int i,j,k,l,m;
double frac = 0. ;
/* Only pointers */
/* Need to be free */
//xsh_localization_list * loc_list = NULL ;
cpl_image* laplacian_image = NULL;
cpl_image* laplacian_redu_image = NULL;
cpl_image* two_sub_sample = NULL;
cpl_image* sci_median5_image = NULL;
cpl_image* noise_image = NULL;
cpl_image* s_image = NULL;
cpl_image* s_median_image = NULL;
cpl_image* s2_image = NULL;
cpl_image* sci_median3_image = NULL;
cpl_image* sci_median3_7_image = NULL;
cpl_image* f_image = NULL;
cpl_image* r_image = NULL;
int two_sub_sample_nx = 0;
int two_sub_sample_ny = 0;
/* Only pointers */
float* sci_data = NULL;
float* two_sub_sample_data = NULL;
float* laplacian_data = NULL;
float* laplacian_redu_data = NULL;
float* sci_median5_data = NULL;
float* sci_median3_data = NULL;
float* sci_median3_7_data = NULL;
float* noise_data = NULL;
float* s_data = NULL;
float* s_median_data = NULL;
float* s2_data = NULL;
float* f_data = NULL;
float* r_data = NULL;
/* Need to be free */
float* cosmic_data = NULL;
cpl_matrix* laplacian_kernel = NULL;
cpl_matrix* median3_kernel = NULL;
cpl_matrix* median5_kernel = NULL;
cpl_matrix* median7_kernel = NULL;
int new_crh =1, nb_crh = 0;
int nbiter = 1 ;
cpl_vector* median = NULL;
//const char * tag = NULL ;
int nx=0;
int ny=0;
cpl_image* res_image=NULL;
/* Check parameters */
cknull( sci_image,"null input image" ) ; ;
sinfo_msg( "Entering sinfo_remove_crh_single");
sinfo_msg( " Params: frac_max %.1f, sigma_lim %.2f f_lim %.2f, iter %d",
crh_frac_max, sigma_lim, f_lim, max_iter);
/* Preparing different kernels */
nx=cpl_image_get_size_x(sci_image);
ny=cpl_image_get_size_y(sci_image);
/* Laplacian */
check_nomsg( laplacian_kernel = cpl_matrix_new(3,3));
cpl_matrix_set( laplacian_kernel,0,0,0.0);
cpl_matrix_set( laplacian_kernel,0,1,-1.0);
cpl_matrix_set( laplacian_kernel,0,2,0.0);
cpl_matrix_set( laplacian_kernel,1,0,-1.0);
cpl_matrix_set( laplacian_kernel,1,1,4.0);
cpl_matrix_set( laplacian_kernel,1,2,-1.0);
cpl_matrix_set( laplacian_kernel,2,0,0.0);
cpl_matrix_set( laplacian_kernel,2,1,-1.0);
cpl_matrix_set( laplacian_kernel,2,2,0.0);
cpl_matrix_divide_scalar( laplacian_kernel, 4.0);
/*
cpl_matrix_set( laplacian_kernel,0,0,-1.0);
cpl_matrix_set( laplacian_kernel,0,1,-1.0);
cpl_matrix_set( laplacian_kernel,0,2,-1.0);
cpl_matrix_set( laplacian_kernel,1,0,-1.0);
cpl_matrix_set( laplacian_kernel,1,1,8.0);
cpl_matrix_set( laplacian_kernel,1,2,-1.0);
cpl_matrix_set( laplacian_kernel,2,0,-1.0);
cpl_matrix_set( laplacian_kernel,2,1,-1.0);
cpl_matrix_set( laplacian_kernel,2,2,-1.0);
cpl_matrix_divide_scalar( laplacian_kernel, 8.0);
*/
/* Median 3x3*/
check_nomsg( median3_kernel = cpl_matrix_new(3,3));
for(j=0; j< 3; j++){
for(i=0; i< 3; i++){
cpl_matrix_set( median3_kernel, i,j,1.0);
}
}
/* Median 5x5 */
check_nomsg( median5_kernel = cpl_matrix_new(5,5));
for(j=0; j< 5; j++){
for(i=0; i< 5; i++){
cpl_matrix_set( median5_kernel, i,j,1.0);
}
}
/* Median 7x7 */
check_nomsg( median7_kernel = cpl_matrix_new(7,7));
for(j=0; j< 7; j++){
for(i=0; i< 7; i++){
cpl_matrix_set( median7_kernel, i,j,1.0);
}
}
check_nomsg (res_image = cpl_image_duplicate( sci_image));
/* Allocate images and pointers */
check_nomsg (sci_data = cpl_image_get_data_float( res_image));
two_sub_sample_nx = nx*2;
two_sub_sample_ny = ny*2;
check_nomsg( two_sub_sample = cpl_image_new( two_sub_sample_nx,
two_sub_sample_ny, CPL_TYPE_FLOAT));
check_nomsg(two_sub_sample_data = cpl_image_get_data_float( two_sub_sample));
check_nomsg( laplacian_redu_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg(laplacian_redu_data = cpl_image_get_data_float(
laplacian_redu_image));
check_nomsg( noise_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg( noise_data = cpl_image_get_data_float( noise_image));
check_nomsg( s_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg( s_data = cpl_image_get_data_float( s_image));
check_nomsg( s2_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg( s2_data = cpl_image_get_data_float( s2_image));
check_nomsg( f_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg( f_data = cpl_image_get_data_float( f_image));
check_nomsg( r_image = cpl_image_new(nx,ny, CPL_TYPE_FLOAT));
check_nomsg( r_data = cpl_image_get_data_float( r_image));
cosmic_data=cpl_calloc(nx*ny, sizeof(float));
/* LGG - Added limit on frac_max AND limit on nb iterations */
while( new_crh > 0 && frac < crh_frac_max && nbiter <= max_iter ){
sinfo_msg("Iteration %d",nbiter );
/* Create a 2n x 2n images like this
| 1 | 2 | => | 1 | 1 | 2 | 2 |
| 3 | 4 | | 1 | 1 | 2 | 2 |
| 3 | 3 | 4 | 4 |
| 3 | 3 | 4 | 4 | */
sinfo_msg_debug("Create a 2n images");
for( j=0; j< ny; j++){
for( i=0; i< nx; i++){
float val = sci_data[i+j*nx];
if ( val < 0. ) val = 0. ;
two_sub_sample_data[i*2+j*2*two_sub_sample_nx] = val;
two_sub_sample_data[i*2+1+j*2*two_sub_sample_nx] = val;
two_sub_sample_data[i*2+(j*2+1)*two_sub_sample_nx] = val;
two_sub_sample_data[i*2+1+(j*2+1)*two_sub_sample_nx] = val;
}
}
sinfo_msg_debug("Doing laplacian convolution");
/* Doing the laplacian convolution
0 -1 0
-1 4 -1
0 -1 0 */
laplacian_image = sinfo_image_filter_linear( two_sub_sample,
laplacian_kernel);
/* multiply by two to normalize correctly the laplacian [RD5]
and filter negative values */
sinfo_msg_debug("Normalize laplacian");
check_nomsg (laplacian_data = cpl_image_get_data_float( laplacian_image));
for ( i=0; i< two_sub_sample_nx*two_sub_sample_ny; i++){
if (laplacian_data[i] > 0.0){
laplacian_data[i] = 2.0 * laplacian_data[i];
}
else{
laplacian_data[i] = 0.0;
}
}
sinfo_msg_debug("Save Lpositive");
cpl_image_save(laplacian_image, "Lpositive.fits", CPL_BPP_IEEE_FLOAT, NULL,
CPL_IO_DEFAULT);
/* resample to the original size
| 1 | 1 | 2 | 2 | | 1 | 2 |
| 1 | 1 | 2 | 2 | | 3 | 4 |
| 3 | 3 | 4 | 4 | =>
| 3 | 3 | 4 | 4 | */
sinfo_msg_debug("Resample to the original size");
for( j=0; j< ny; j++){
for( i=0; i< nx; i++){
laplacian_redu_data[i+j*nx] =
(laplacian_data[i*2+j*2*two_sub_sample_nx]+
laplacian_data[i*2+1+j*2*two_sub_sample_nx]+
laplacian_data[i*2+(j*2+1)*two_sub_sample_nx]+
laplacian_data[i*2+1+(j*2+1)*two_sub_sample_nx])/4.0;
}
}
cpl_image_save(laplacian_redu_image, "Lplus.fits", CPL_BPP_IEEE_FLOAT,
NULL, CPL_IO_DEFAULT);
sinfo_msg_debug("Apply median filter");
/* Apply 5x5 median filter on data */
check_nomsg( sci_median5_image = sinfo_image_filter_median( sci_image,
median5_kernel));
check_nomsg (sci_median5_data = cpl_image_get_data_float( sci_median5_image));
sinfo_msg_debug("Compute noise");
/* computes the noise image */
for( i=0; i< nx*ny; i++){
noise_data[i] = sqrt(sci_median5_data[i]*gain+
ron*ron)/ gain;
}
sinfo_msg_debug("Compute S");
/* compute S image */
for( i=0; i< nx*ny; i++){
s_data[i] = laplacian_redu_data[i] / (2.0*noise_data[i]);
}
sinfo_msg_debug("Compute S median");
/* compute S median image */
check_nomsg( s_median_image = sinfo_image_filter_median( s_image,
median5_kernel));
check_nomsg( s_median_data = cpl_image_get_data_float( s_median_image));
sinfo_msg_debug("Compute s2");
/* compute s2 */
for( i=0; i< nx*ny; i++){
s2_data[i] = s_data[i] -s_median_data[i];
}
cpl_image_save( s2_image, "S2.fits", CPL_BPP_IEEE_FLOAT, NULL,
CPL_IO_DEFAULT);
sinfo_msg_debug("Apply 3x3 filter");
/* Apply 3x3 median filter on data */
check_nomsg( sci_median3_image = sinfo_image_filter_median( sci_image,
median3_kernel));
sinfo_msg_debug("Apply 7x7 filter");
/* Apply 7x7 median filter */
check_nomsg( sci_median3_7_image = sinfo_image_filter_median( sci_median3_image,
median7_kernel));
sinfo_msg_debug("Apply 7x7 filter ok");
check_nomsg ( sci_median3_data = cpl_image_get_data_float( sci_median3_image));
check_nomsg ( sci_median3_7_data = cpl_image_get_data_float(
sci_median3_7_image));
sinfo_msg_debug("Compute F");
/* compute F */
for( i=0; i< nx*ny; i++){
f_data[i] = sci_median3_data[i] -sci_median3_7_data[i];
if (f_data[i] < 0.01){
f_data[i] = 0.01;
}
}
cpl_image_save( f_image, "F.fits", CPL_BPP_IEEE_FLOAT, NULL,
CPL_IO_DEFAULT);
sinfo_msg_debug("Compute R");
/* compute R */
for( i=0; i< nx*ny; i++){
r_data[i] = laplacian_redu_data[i]/f_data[i];
}
cpl_image_save( r_image, "R.fits", CPL_BPP_IEEE_FLOAT, NULL,
CPL_IO_DEFAULT);
/* Search for cosmics */
sinfo_msg_debug("Search for cosmic");
new_crh = 0;
median = cpl_vector_new(24);
for( j=1; j< ny-1; j++){
double *data = NULL;
cpl_vector* med_vect = NULL;
for( i=1; i< nx-1; i++){
if ( (s2_data[i+j*nx] >= sigma_lim) &&
(r_data[i+j*nx] >= f_lim)){
int li,lj,ui,uj;
cosmic_data[i+j*nx] = 1.0;
new_crh++;
li = i-2;
lj = j-2;
ui = i+2;
uj = j+2;
m = 0;
if (li < 0) li = 0;
if (ui >= nx) ui = nx-1;
if (lj < 0) lj = 0;
if (uj >= ny) uj = ny-1;
for( k=lj; k <= uj; k++){
for( l=li; l <= ui; l++){
//sinfo_msg("REGDEBUG k %d l %d m %d", k, l, m);
if ( k < j){
cpl_vector_set(median, m, sci_data[l+k*nx]);
m++;
}
else if ( (k == j) && ( l < i)){
cpl_vector_set(median, m, sci_data[l+k*nx]);
m++;
}
else if ( l!=i && k!=j && (s2_data[l+k*nx] < sigma_lim)
&& (r_data[l+k*nx] < f_lim)){
cpl_vector_set(median, m, sci_data[l+k*nx]);
m++;
}
}
}
check_nomsg( data = cpl_vector_get_data( median));
sinfo_msg_debug("REGDEBUG i %d j %d m %d", i, j ,m);
check_nomsg( med_vect = cpl_vector_wrap( m, data));
check_nomsg( sci_data[i+j*nx] = cpl_vector_get_median( med_vect));
cpl_vector_unwrap( med_vect);
}
}
}
sinfoni_free_vector( &median ) ;
nb_crh += new_crh;
frac = (double)nb_crh/(double)(nx*ny) ;
sinfo_msg(" new cosmics %d, total %d, frac %.4f [%d pixels]",new_crh,nb_crh,
frac, nx*ny);
nbiter++;
sinfo_free_image( &laplacian_image);
sinfo_free_image( &sci_median3_7_image ) ;
sinfo_free_image( &sci_median3_image ) ;
sinfo_free_image( &s_median_image ) ;
sinfo_free_image( &sci_median5_image ) ;
}
{
FILE *debug = NULL;
debug = fopen("cosmic.log","w");
for( j=0; j< ny; j++){
for( i=0; i< nx; i++){
if ( cosmic_data[i+j*nx] == 1.0){
fprintf(debug,"%.1f %.1f\n",i+1.0,j+1.0);
}
}
}
fclose(debug);
}
//check_nomsg( res_frame = cpl_frame_duplicate( sci_frame ) ) ;
//sinfo_msg( "Saving Result Frame '%s'", res_name ) ;
//check_nomsg( add_qc_crh( sci_pre, nb_crh, 1, instrument ) ) ;
//check_nomsg( res_frame = xsh_pre_save( sci_pre, res_name, 1 ) ) ;
//tag = cpl_frame_get_tag( in_sci_frame ) ;
//check_nomsg( cpl_frame_set_tag( res_frame, tag ) ) ;
cleanup:
//xsh_pre_free( &sci_pre);
//xsh_localization_list_free( &loc_list ) ;
/* free kernel */
sinfoni_free_matrix( &laplacian_kernel);
sinfoni_free_matrix( &median3_kernel);
sinfoni_free_matrix( &median5_kernel);
sinfoni_free_matrix( &median7_kernel);
/* free images */
sinfo_free_image( &laplacian_image);
sinfo_free_image( &laplacian_redu_image);
sinfo_free_image( &two_sub_sample);
sinfo_free_image( &sci_median5_image);
sinfo_free_image( &noise_image);
sinfo_free_image( &s_image);
sinfo_free_image( &s_median_image);
sinfo_free_image( &s2_image);
sinfo_free_image( &sci_median3_image);
sinfo_free_image( &sci_median3_7_image);
sinfo_free_image( &f_image);
sinfo_free_image( &r_image);
/* free vector */
sinfoni_free_vector( &median);
/* free tab */
if(cosmic_data!=NULL) cpl_free( cosmic_data);
return res_image;
}
/**@}*/
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