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/*
* This file is part of the ESO SINFONI Pipeline
* Copyright (C) 2004,2005 European Southern Observatory
*
* This program 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
*/
/*----------------------------------------------------------------------------
File name : sinfo_bp_lin.c
Author : J. Schreiber
Created on : May 5, 2003
Description : Different methods for searching for bad pixels
used in the recipe spiffi_badsearch
---------------------------------------------------------------------------*/
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
/*----------------------------------------------------------------------------
Includes
---------------------------------------------------------------------------*/
//#include <cpl_imagelist_basic.h>
#include <cpl.h>
#include "sinfo_bp_lin.h"
#include "sinfo_detlin.h"
#include "sinfo_detlin_ini_by_cpl.h"
#include "sinfo_pro_save.h"
#include "sinfo_pro_types.h"
#include "sinfo_functions.h"
#include "sinfo_hidden.h"
#include "sinfo_error.h"
#include "sinfo_utils_wrappers.h"
/**
* @addtogroup sinfo_bad_pix_search Bad Pixel Search
*
* TBD
*/
/*----------------------------------------------------------------------------
Defines
---------------------------------------------------------------------------*/
/*----------------------------------------------------------------------------
Function Definitions
---------------------------------------------------------------------------*/
/**
@name sinfo_new_bp_search_lin
@memo Search pixels which have a non linear response
@param plugin_id recipe name
@param config input parameters list
@param sof input set of frames
@returns integer (0 if it worked, -1 if it doesn't)
@doc
this function searches for static bad pixels in stacks of flatfield frames
with in/decreasing intensities. For each pixel position a curve is plotted
of the pixel intensity in each plane against the clean mean of the whole
plane.
A polynomial is fit and the found coefficients are stored sequentially in
a data cube. Then the deviation of the linear coefficients from the clean
mean is computed for each pixel and the pixel are declared bad if the
deviations exceed a threshold defined by a factor of the clean standard
deviation.
For the resting good pixels the non-linear coefficients are examined.
If one coefficients deviate more than a user given threshold the pixel
is also declared as bad. The data cubus with the fit results and
a bad pixel mask image is stored
*/
int
sinfo_new_bp_search_lin(const char* plugin_id,
cpl_parameterlist* config,
cpl_frameset* sof)
{
detlin_config * cfg=NULL;
cpl_imagelist * imgl=NULL ;
cpl_imagelist * coeffs_imgl=NULL;
cpl_image * img_tmp=NULL ;
cpl_image * mask=NULL;
cpl_vector* cube_mean=NULL;
cpl_frameset* raw=NULL;
cpl_frameset* raw_on=NULL;
cpl_frameset* raw_of=NULL;
cpl_frame* frm=NULL;
cpl_frame* frm_dup=NULL;
cpl_table* qclog_tbl=NULL;
cpl_parameter *p=NULL;
cpl_polynomial *pol=NULL;
cpl_vector* vec_adl=NULL;
cpl_vector* vec_med=NULL;
double* mse=NULL;
int i=0;
int n_bad=0 ;
int nff=0;
char key_value[FILE_NAME_SZ];
char key_name[FILE_NAME_SZ];
cpl_table* det_lin=NULL;
int nraw=0;
int* status=NULL;
cpl_table* gain=NULL;
int ngain=0;
int sz_imgl=0;
/*
int llx=270;
int lly=1030;
int urx=310;
int ury=1060;
*/
//int zone[4];
//int kappa=5;
//int nclip=25;
int pdensity=0;
check_nomsg(p=cpl_parameterlist_find(config,"sinfoni.product.density"));
check_nomsg(pdensity=cpl_parameter_get_int(p));
/* parse the file names and parameters to the bad_config
data structure cfg */
check_nomsg(raw=cpl_frameset_new());
cknull(cfg = sinfo_parse_cpl_input_detlin(config,sof,&raw),
"could not parse .ini file!");
/* ======================================================================
DETERMINES LINEARITY COEFF AS DFO DOES
======================================================================
*/
nff=cpl_frameset_get_size(raw);
raw_on=cpl_frameset_new();
raw_of=cpl_frameset_new();
/* separates on and off frames */
for(i=0;i<nff;i++) {
frm=cpl_frameset_get_frame(raw,i);
frm_dup=cpl_frame_duplicate(frm);
if(sinfo_frame_is_on(frm)) {
cpl_frameset_insert(raw_on,frm_dup);
} else {
cpl_frameset_insert(raw_of,frm_dup);
}
}
/*
cknull(det_lin=sinfo_get_linearity(raw_on,raw_of),
"Error computing linearity");
*/
/*
zone[0]=llx;
zone[1]=lly;
zone[2]=urx;
zone[3]=ury;
*/
//If one refers to a larger area
/*
zone[0]=20;
zone[1]=2028;
zone[2]=20;
zone[3]=2028;
*/
/*
cknull(det_lin=irplib_compute_linearity(raw_on,raw_of),
"Error computing linearity");
*/
if(pdensity > 1 ) {
sinfo_msg("Computes linearity");
cknull(det_lin=sinfo_compute_linearity(raw_on,raw_of),
"Error computing linearity");
check_nomsg(nraw=cpl_table_get_nrow(det_lin));
check_nomsg(vec_adl=cpl_vector_new(nraw));
check_nomsg(vec_med=cpl_vector_new(nraw));
for(i=0;i<nraw;i++) {
cpl_vector_set(vec_adl,i,cpl_table_get_double(det_lin,"adl",i,status));
cpl_vector_set(vec_med,i,cpl_table_get_double(det_lin,"med",i,status));
}
check_nomsg(pol=sinfo_polynomial_fit_1d_create(vec_adl,vec_med,
cfg->order,mse));
sinfo_free_my_vector(&vec_adl);
sinfo_free_my_vector(&vec_med);
cknull_nomsg(qclog_tbl=sinfo_qclog_init());
cpl_size deg=0;
for(deg=0;deg<cfg->order+1;deg++) {
snprintf(key_name,MAX_NAME_SIZE-1,"%s%" CPL_SIZE_FORMAT "%s",
"QC BP-MAP LIN",deg," MED");
sinfo_qclog_add_double(qclog_tbl,key_name,
cpl_polynomial_get_coeff(pol,°),
"Linearity Polynomial Coeff","%g");
}
sinfo_free_polynomial(&pol);
check_nomsg(p = cpl_parameterlist_find(config, "sinfoni.bp.method"));
snprintf(key_value, MAX_NAME_SIZE-1,"%s",cpl_parameter_get_string(p));
ck0_nomsg(sinfo_qclog_add_string(qclog_tbl,"QC BP-MAP METHOD",key_value,
"BP search method","%s"));
ck0(sinfo_pro_save_tbl(det_lin,raw,sof,BP_LIN_LIN_DET_INFO_OUT_FILENAME,
PRO_LIN_DET_INFO,qclog_tbl,plugin_id,config),
"cannot dump ims %s",BP_LIN_LIN_DET_INFO_OUT_FILENAME);
sinfo_free_table(&det_lin);
sinfo_free_table(&qclog_tbl);
}
/*=======================================================*/
if(pdensity > 1 ) {
sinfo_msg("Computes gain");
cknull(gain=sinfo_compute_gain(raw_on,raw_of),"Error computing gain");
//cknull(gain=irplib_compute_gain(raw_on,raw_of,zone,kappa,nclip),
// "Error computing gain");
sinfo_free_frameset(&raw_on);
sinfo_free_frameset(&raw_of);
check_nomsg(ngain=cpl_table_get_nrow(gain));
cknull_nomsg(qclog_tbl=sinfo_qclog_init());
for(i=0;i<ngain;i++) {
snprintf(key_name,MAX_NAME_SIZE-1,"%s%i","QC GAIN",i);
ck0_nomsg(sinfo_qclog_add_double(qclog_tbl,key_name,
cpl_table_get_double(gain,"gain",i,status),
"Detector gain","%g"));
}
ck0_nomsg(sinfo_qclog_add_double(qclog_tbl,"QC GAIN",
cpl_table_get_column_median(gain,"gain"),
"Detector gain median","%g"));
ck0_nomsg(sinfo_qclog_add_double(qclog_tbl,"QC GAINERR",
cpl_table_get_column_stdev(gain,"gain"),
"Detector gain error","%g"));
ck0(sinfo_pro_save_tbl(gain,raw,sof,BP_LIN_GAIN_OUT_FILENAME,
PRO_GAIN_INFO,qclog_tbl,plugin_id,config),
"cannot dump tbl %s", BP_LIN_GAIN_OUT_FILENAME);
sinfo_free_table(&gain);
sinfo_free_table(&qclog_tbl);
}
/* =======================================================================
DETERMINES LINEARITY COEFF AS MPE DOES
=======================================================================
*/
check_nomsg(imgl = cpl_imagelist_new());
for ( i = 0 ; i < cfg->nframes ; i++ )
{
if(sinfo_is_fits_file (cfg->framelist[i]) != 1) {
sinfo_msg_error("Input file %s is not FITS",cfg->framelist[i] );
return -1;
}
check_nomsg(img_tmp=cpl_image_load(cfg->framelist[i],CPL_TYPE_FLOAT,0,0));
check_nomsg(cpl_imagelist_set(imgl,img_tmp,i));
}
/*----------------------------------------------------------------
*---------------------- SEARCH FOR BAD PIXELS---------------------
*--------------------------------------------------------------*/
sinfo_msg("Search for bad pixels");
cknull(coeffs_imgl=sinfo_new_fit_intensity_course(imgl,
cfg->order,
cfg->loReject,
cfg->hiReject),
"could not fit polynomial and store coeffs in a data cube!");
sinfo_free_imagelist(&imgl) ;
check_nomsg(sz_imgl=cpl_imagelist_get_size(coeffs_imgl));
/*---store the polynomial fit coefficients in a data cube----*/
/* CUBE NOT DUMPED BECAUSE PROBLEMS ON LAST PLANE */
cube_mean=cpl_vector_new(sz_imgl);
/* QC LOG */
cknull_nomsg(qclog_tbl=sinfo_qclog_init());
for(i=0;i<sz_imgl;i++) {
cpl_vector_set(cube_mean,i,
cpl_image_get_median(cpl_imagelist_get(coeffs_imgl,i)));
snprintf(key_name,MAX_NAME_SIZE-1,"%s%i%s","QC BP-MAP LIN",i," MEAN");
snprintf(key_value,MAX_NAME_SIZE-1,"%g",cpl_vector_get(cube_mean,i));
ck0_nomsg(sinfo_qclog_add_double(qclog_tbl,key_name,
cpl_vector_get(cube_mean,i),
"Linearity Polynomial Coeff","%g"));
}
sinfo_free_my_vector(&cube_mean);
check_nomsg(p = cpl_parameterlist_find(config, "sinfoni.bp.method"));
snprintf(key_value, MAX_NAME_SIZE-1,"%s",cpl_parameter_get_string(p));
ck0_nomsg(sinfo_qclog_add_string(qclog_tbl,"QC BP-MAP METHOD",key_value,
"BP search method","%s"));
ck0(sinfo_pro_save_ims(coeffs_imgl,raw,sof,cfg->coeffsCubeName,
PRO_BP_COEFF,qclog_tbl,plugin_id,config),
"cannot dump ims %s", cfg->coeffsCubeName);
sinfo_free_table(&qclog_tbl);
/* =======================================================================
DETERMINES BAD PIXEL MAP
=======================================================================
*/
sinfo_msg("Generates bad pixel map");
cknull(mask = sinfo_new_search_bad_pixels (coeffs_imgl,
cfg->threshSigmaFactor,
cfg->nonlinearThresh,
cfg->loReject,
cfg->hiReject),
"could not create bad pixel mask!") ;
sinfo_free_imagelist(&coeffs_imgl) ;
check_nomsg(n_bad = sinfo_new_count_bad_pixels(mask)) ;
sinfo_msg( "No of bad pixels: %d", n_bad ) ;
/* QC LOG */
cknull_nomsg(qclog_tbl=sinfo_qclog_init());
check_nomsg(p = cpl_parameterlist_find(config, "sinfoni.bp.method"));
snprintf(key_value, MAX_NAME_SIZE-1,"%s",cpl_parameter_get_string(p));
ck0_nomsg(sinfo_qclog_add_string(qclog_tbl,"QC BP-MAP METHOD",key_value,
"BP search method","%s"));
ck0_nomsg(sinfo_qclog_add_int(qclog_tbl,"QC BP-MAP NBADPIX",n_bad,
"No of bad pixels","%d"));
ck0(sinfo_pro_save_ima(mask,raw,sof,cfg->outName,PRO_BP_MAP_NL,qclog_tbl,
plugin_id,config),
"cannot save ima %s", cfg->outName);
/* ======================================================================
FREE MEMORY
======================================================================
*/
sinfo_free_table(&qclog_tbl);
sinfo_free_image(&mask);
sinfo_free_frameset(&raw);
sinfo_detlin_free(&cfg);
return 0;
cleanup:
sinfo_free_frameset(&raw_on);
sinfo_free_frameset(&raw_of);
sinfo_free_image(&mask) ;
sinfo_free_my_vector(&cube_mean);
sinfo_free_imagelist(&imgl);
sinfo_free_imagelist(&coeffs_imgl);
sinfo_free_table(&gain);
sinfo_free_table(&qclog_tbl);
sinfo_free_table(&det_lin);
sinfo_free_my_vector(&vec_adl);
sinfo_free_my_vector(&vec_med);
sinfo_free_polynomial(&pol);
sinfo_detlin_free(&cfg);
sinfo_free_frameset(&raw);
return -1;
}
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