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/*
* makeit.c
*
* Main program.
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2015 Emmanuel Bertin -- IAP/CNRS/UPMC
*
* License: GNU General Public License
*
* SExtractor 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 3 of the License, or
* (at your option) any later version.
* SExtractor 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 SExtractor. If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 21/01/2015
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "define.h"
#include "globals.h"
#include "prefs.h"
#include "fits/fitscat.h"
#include "assoc.h"
#include "back.h"
#include "check.h"
#include "fft.h"
#include "field.h"
#include "filter.h"
#include "growth.h"
#include "interpolate.h"
#include "pattern.h"
#include "psf.h"
#include "profit.h"
#include "som.h"
#include "weight.h"
#include "xml.h"
static int selectext(char *filename);
time_t thetimet, thetimet2;
#ifdef USE_MODEL
extern profitstruct *theprofit,*thedprofit, *thepprofit,*theqprofit;
#else
profitstruct *theprofit,*thedprofit, *thepprofit,*theqprofit;
#endif
extern char profname[][32];
double dtime;
/******************************** makeit *************************************/
/*
Manage the whole stuff.
*/
void makeit()
{
checkstruct *check;
picstruct *dfield, *field,*pffield[MAXFLAG], *wfield,*dwfield,
*dgeofield;
catstruct *imacat;
tabstruct *imatab;
patternstruct *pattern;
static time_t thetime1, thetime2;
struct tm *tm;
unsigned int modeltype;
int nflag[MAXFLAG], nparam2[2],
i, nok, ntab, next, ntabmax, forcextflag,
nima0,nima1, nweight0,nweight1, npsf0,npsf1, npat,npat0,
ndgeo;
/* Install error logging */
error_installfunc(write_error);
/* Processing start date and time */
dtime = counter_seconds();
thetimet = time(NULL);
tm = localtime(&thetimet);
sprintf(prefs.sdate_start,"%04d-%02d-%02d",
tm->tm_year+1900, tm->tm_mon+1, tm->tm_mday);
sprintf(prefs.stime_start,"%02d:%02d:%02d",
tm->tm_hour, tm->tm_min, tm->tm_sec);
NFPRINTF(OUTPUT, "");
QPRINTF(OUTPUT, "----- %s %s started on %s at %s with %d thread%s\n\n",
BANNER,
MYVERSION,
prefs.sdate_start,
prefs.stime_start,
prefs.nthreads,
prefs.nthreads>1? "s":"");
/* Initialize globals variables */
initglob();
NFPRINTF(OUTPUT, "Setting catalog parameters");
readcatparams(prefs.param_name);
useprefs(); /* update things accor. to prefs parameters */
/* Check if a specific extension should be loaded */
if ((nima0=selectext(prefs.image_name[0])) != RETURN_ERROR)
{
forcextflag = 1;
ntabmax = next = 1;
}
else
forcextflag = 0;
/* Do the same for other data (but do not force single extension mode) */
nima1 = selectext(prefs.image_name[1]);
nweight0 = selectext(prefs.wimage_name[0]);
nweight1 = selectext(prefs.wimage_name[1]);
if (prefs.dpsf_flag)
{
npsf0 = selectext(prefs.psf_name[0]);
npsf1 = selectext(prefs.psf_name[1]);
}
else
npsf0 = selectext(prefs.psf_name[0]);
for (i=0; i<prefs.nfimage_name; i++)
nflag[i] = selectext(prefs.fimage_name[i]);
ndgeo = selectext(prefs.dgeoimage_name);
if (prefs.psf_flag)
{
/*-- Read the first PSF extension to set up stuff such as context parameters */
NFPRINTF(OUTPUT, "Reading PSF information");
if (prefs.dpsf_flag)
{
thedpsf = psf_load(prefs.psf_name[0],nima0<0? 1 :(npsf0<0? 1:npsf0));
thepsf = psf_load(prefs.psf_name[1], nima1<0? 1 :(npsf1<0? 1:npsf1));
}
else
thepsf = psf_load(prefs.psf_name[0], nima0<0? 1 :(npsf0<0? 1:npsf0));
/*-- Need to check things up because of PSF context parameters */
updateparamflags();
useprefs();
}
if (prefs.prof_flag)
{
#ifdef USE_MODEL
fft_init(prefs.nthreads);
/* Create profiles at full resolution */
NFPRINTF(OUTPUT, "Preparing profile models");
modeltype = (FLAG(obj2.prof_offset_flux)? MODEL_BACK : MODEL_NONE)
|(FLAG(obj2.prof_dirac_flux)? MODEL_DIRAC : MODEL_NONE)
|(FLAG(obj2.prof_spheroid_flux)?
(FLAG(obj2.prof_spheroid_sersicn)?
MODEL_SERSIC : MODEL_DEVAUCOULEURS) : MODEL_NONE)
|(FLAG(obj2.prof_disk_flux)? MODEL_EXPONENTIAL : MODEL_NONE)
|(FLAG(obj2.prof_bar_flux)? MODEL_BAR : MODEL_NONE)
|(FLAG(obj2.prof_arms_flux)? MODEL_ARMS : MODEL_NONE);
theprofit = profit_init(thepsf, modeltype);
changecatparamarrays("VECTOR_MODEL", &theprofit->nparam, 1);
changecatparamarrays("VECTOR_MODELERR", &theprofit->nparam, 1);
nparam2[0] = nparam2[1] = theprofit->nparam;
changecatparamarrays("MATRIX_MODELERR", nparam2, 2);
if (prefs.dprof_flag)
thedprofit = profit_init(thedpsf, modeltype);
if (prefs.pattern_flag)
{
npat0 = prefs.prof_disk_patternvectorsize;
if (npat0<prefs.prof_disk_patternmodvectorsize)
npat0 = prefs.prof_disk_patternmodvectorsize;
if (npat0<prefs.prof_disk_patternargvectorsize)
npat0 = prefs.prof_disk_patternargvectorsize;
/*---- Do a copy of the original number of pattern components */
prefs.prof_disk_patternncomp = npat0;
pattern = pattern_init(theprofit, prefs.pattern_type, npat0);
if (FLAG(obj2.prof_disk_patternvector))
{
npat = pattern->size[2];
changecatparamarrays("DISK_PATTERN_VECTOR", &npat, 1);
}
if (FLAG(obj2.prof_disk_patternmodvector))
{
npat = pattern->ncomp*pattern->nfreq;
changecatparamarrays("DISK_PATTERNMOD_VECTOR", &npat, 1);
}
if (FLAG(obj2.prof_disk_patternargvector))
{
npat = pattern->ncomp*pattern->nfreq;
changecatparamarrays("DISK_PATTERNARG_VECTOR", &npat, 1);
}
pattern_end(pattern);
}
QPRINTF(OUTPUT, "Fitting model: ");
for (i=0; i<theprofit->nprof; i++)
{
if (i)
QPRINTF(OUTPUT, "+");
QPRINTF(OUTPUT, "%s", theprofit->prof[i]->name);
}
QPRINTF(OUTPUT, "\n");
if (FLAG(obj2.prof_concentration)|FLAG(obj2.prof_concentration))
{
thepprofit = profit_init(thepsf, MODEL_DIRAC);
theqprofit = profit_init(thepsf, MODEL_EXPONENTIAL);
}
#else
error(EXIT_FAILURE,
"*Error*: model-fitting is not supported in this build.\n",
" Please check your configure options");
#endif
}
if (prefs.filter_flag)
{
NFPRINTF(OUTPUT, "Reading detection filter");
getfilter(prefs.filter_name); /* get the detection filter */
}
if (FLAG(obj2.sprob))
{
NFPRINTF(OUTPUT, "Initializing Neural Network");
neurinit();
NFPRINTF(OUTPUT, "Reading Neural Network Weights");
getnnw();
}
if (prefs.somfit_flag)
{
int margin;
thesom = som_load(prefs.som_name);
if ((margin=(thesom->inputsize[1]+1)/2) > prefs.cleanmargin)
prefs.cleanmargin = margin;
if (prefs.somfit_vectorsize>thesom->neurdim)
{
prefs.somfit_vectorsize = thesom->neurdim;
sprintf(gstr,"%d", prefs.somfit_vectorsize);
warning("Dimensionality of the SOM-fit vector limited to ", gstr);
}
}
/* Prepare growth-curve buffer */
if (prefs.growth_flag)
initgrowth();
/* Allocate memory for multidimensional catalog parameter arrays */
alloccatparams();
useprefs();
if (!(imacat = read_cat(prefs.image_name[0])))
error(EXIT_FAILURE, "*Error*: cannot open ", prefs.image_name[0]);
close_cat(imacat);
imatab = imacat->tab;
if (!forcextflag)
{
ntabmax = imacat->ntab;
/*-- Compute the number of valid input extensions */
next = 0;
for (ntab = 0 ; ntab<imacat->ntab; ntab++, imatab = imatab->nexttab)
{
/*---- Check for the next valid image extension */
if ((imatab->naxis < 2)
|| !strncmp(imatab->xtension, "BINTABLE", 8)
|| !strncmp(imatab->xtension, "ASCTABLE", 8))
continue;
next++;
}
}
thecat.next = next;
/*-- Init the CHECK-images */
if (prefs.check_flag)
{
checkenum c;
NFPRINTF(OUTPUT, "Initializing check-image(s)");
for (i=0; i<prefs.ncheck_type; i++)
if ((c=prefs.check_type[i]) != CHECK_NONE)
{
if (prefs.check[c])
error(EXIT_FAILURE,"*Error*: 2 CHECK_IMAGEs cannot have the same ",
" CHECK_IMAGE_TYPE");
prefs.check[c] = initcheck(prefs.check_name[i], prefs.check_type[i],
next);
}
}
NFPRINTF(OUTPUT, "Initializing catalog");
initcat();
/* Initialize XML data */
if (prefs.xml_flag || prefs.cat_type==ASCII_VO)
init_xml(next);
/* Go through all images */
nok = 0;
for (ntab = 0 ; ntab<ntabmax; ntab++, imatab = imatab->nexttab)
{
/*-- Check for the next valid image extension */
if (!forcextflag && ((imatab->naxis < 2)
|| !strncmp(imatab->xtension, "BINTABLE", 8)
|| !strncmp(imatab->xtension, "ASCTABLE", 8)))
continue;
nok++;
/*-- Initial time measurement*/
time(&thetime1);
thecat.currext = nok;
dfield = field = wfield = dwfield = dgeofield = NULL;
if (prefs.dimage_flag)
{
/*---- Init the Detection and Measurement-images */
dfield = newfield(prefs.image_name[0], DETECT_FIELD,
nima0<0? ntab:nima0);
field = newfield(prefs.image_name[1], MEASURE_FIELD,
nima1<0? ntab:nima1);
if ((field->width!=dfield->width) || (field->height!=dfield->height))
error(EXIT_FAILURE, "*Error*: Frames have different sizes","");
/*---- Prepare interpolation */
if (prefs.dweight_flag && prefs.interp_type[0] == INTERP_ALL)
init_interpolate(dfield, -1, -1);
if (prefs.interp_type[1] == INTERP_ALL)
init_interpolate(field, -1, -1);
}
else
{
field = newfield(prefs.image_name[0], DETECT_FIELD | MEASURE_FIELD,
nima0<0? ntab:nima0);
/*---- Prepare interpolation */
if ((prefs.dweight_flag || prefs.weight_flag)
&& prefs.interp_type[0] == INTERP_ALL)
init_interpolate(field, -1, -1); /* 0.0 or anything else */
}
/*-- Init the WEIGHT-images */
if (prefs.dweight_flag || prefs.weight_flag)
{
weightenum wtype;
PIXTYPE interpthresh;
if (prefs.nweight_type>1)
{
/*------ Double-weight-map mode */
if (prefs.weight_type[1] != WEIGHT_NONE)
{
/*-------- First: the "measurement" weights */
wfield = newweight(prefs.wimage_name[1],field,prefs.weight_type[1],
(nima1<0 && prefs.image_name[1])?
ntab : (nweight1<0?1:nweight1));
wtype = prefs.weight_type[1];
interpthresh = prefs.weight_thresh[1];
/*-------- Convert the interpolation threshold to variance units */
weight_to_var(wfield, &interpthresh, 1);
wfield->weight_thresh = interpthresh;
if (prefs.interp_type[1] != INTERP_NONE)
init_interpolate(wfield,
prefs.interp_xtimeout[1], prefs.interp_ytimeout[1]);
}
/*------ The "detection" weights */
if (prefs.weight_type[0] != WEIGHT_NONE)
{
interpthresh = prefs.weight_thresh[0];
if (prefs.weight_type[0] == WEIGHT_FROMINTERP)
{
dwfield=newweight(prefs.wimage_name[0],wfield,prefs.weight_type[0],
nima0<0? ntab : (nweight0<0? 1 :nweight0));
weight_to_var(wfield, &interpthresh, 1);
}
else
{
dwfield = newweight(prefs.wimage_name[0], dfield?dfield:field,
prefs.weight_type[0], nima0<0? ntab : (nweight0<0?1:nweight0));
weight_to_var(dwfield, &interpthresh, 1);
}
dwfield->weight_thresh = interpthresh;
if (prefs.interp_type[0] != INTERP_NONE)
init_interpolate(dwfield,
prefs.interp_xtimeout[0], prefs.interp_ytimeout[0]);
}
}
else
{
/*------ Single-weight-map mode */
wfield = newweight(prefs.wimage_name[0], dfield?dfield:field,
prefs.weight_type[0], nima0<0? ntab : (nweight0<0?1:nweight0));
wtype = prefs.weight_type[0];
interpthresh = prefs.weight_thresh[0];
/*------ Convert the interpolation threshold to variance units */
weight_to_var(wfield, &interpthresh, 1);
wfield->weight_thresh = interpthresh;
if (prefs.interp_type[0] != INTERP_NONE)
init_interpolate(wfield,
prefs.interp_xtimeout[0], prefs.interp_ytimeout[0]);
}
}
/*-- Init the FLAG-images */
for (i=0; i<prefs.nimaflag; i++)
{
pffield[i] = newfield(prefs.fimage_name[i], FLAG_FIELD,
nima0<0? ntab : (nflag[i]<0?1:nflag[i]));
if ((pffield[i]->width!=field->width)
|| (pffield[i]->height!=field->height))
error(EXIT_FAILURE,
"*Error*: Incompatible FLAG-map size in ", prefs.fimage_name[i]);
}
/*-- Init the differential geometry images */
if (prefs.dgeo_type != DGEO_NONE) {
dgeofield = newfield(prefs.dgeoimage_name, DGEO_FIELD,
nima0<0? ntab : (ndgeo<0?1:ndgeo));
if ((dgeofield->width != field->width)
|| (dgeofield->height != field->height))
error(EXIT_FAILURE,
"*Error*: Incompatible differential geometry map size in ",
prefs.dgeoimage_name);
}
/*-- Compute background maps for `standard' fields */
QPRINTF(OUTPUT, dfield? "Measurement image:"
: "Detection+Measurement image: ");
makeback(field, wfield, prefs.wscale_flag[1]);
QPRINTF(OUTPUT, (dfield || (dwfield&&dwfield->flags^INTERP_FIELD))? "(M) "
"Background: %-10g RMS: %-10g / Threshold: %-10g \n"
: "(M+D) "
"Background: %-10g RMS: %-10g / Threshold: %-10g \n",
field->backmean, field->backsig, (field->flags & DETECT_FIELD)?
field->dthresh: field->thresh);
if (dfield)
{
QPRINTF(OUTPUT, "Detection image: ");
makeback(dfield, dwfield? dwfield
: (prefs.weight_type[0] == WEIGHT_NONE?NULL:wfield),
prefs.wscale_flag[0]);
QPRINTF(OUTPUT, "(D) "
"Background: %-10g RMS: %-10g / Threshold: %-10g \n",
dfield->backmean, dfield->backsig, dfield->dthresh);
}
else if (dwfield && dwfield->flags^INTERP_FIELD)
{
makeback(field, dwfield, prefs.wscale_flag[0]);
QPRINTF(OUTPUT, "(D) "
"Background: %-10g RMS: %-10g / Threshold: %-10g \n",
field->backmean, field->backsig, field->dthresh);
}
/*-- For interpolated weight-maps, copy the background structure */
if (dwfield && dwfield->flags&(INTERP_FIELD|BACKRMS_FIELD))
copyback(dwfield->reffield, dwfield);
if (wfield && wfield->flags&(INTERP_FIELD|BACKRMS_FIELD))
copyback(wfield->reffield, wfield);
/*-- Prepare learn and/or associations */
if (prefs.assoc_flag)
init_assoc(field); /* initialize assoc tasks */
/*-- Update the CHECK-images */
if (prefs.check_flag)
for (i=0; i<MAXCHECK; i++)
if ((check=prefs.check[i]))
reinitcheck(field, check);
if (!forcextflag && nok>1)
{
if (prefs.psf_flag)
{
/*------ Read other PSF extensions */
NFPRINTF(OUTPUT, "Reading PSF information");
psf_end(thepsf, thepsfit);
if (prefs.dpsf_flag)
{
psf_end(thedpsf, thedpsfit);
thedpsf = psf_load(prefs.psf_name[0], nok);
thepsf = psf_load(prefs.psf_name[1], nok);
}
else
thepsf = psf_load(prefs.psf_name[0], nok);
}
#ifdef USE_MODEL
if (prefs.prof_flag)
{
/*------ Create profiles at full resolution */
profit_end(theprofit);
theprofit = profit_init(thepsf, modeltype);
if (prefs.dprof_flag)
{
profit_end(thedprofit);
thedprofit = profit_init(thedpsf, modeltype);
}
if (prefs.pattern_flag)
{
pattern = pattern_init(theprofit, prefs.pattern_type, npat0);
pattern_end(pattern);
}
if (FLAG(obj2.prof_concentration)|FLAG(obj2.prof_concentration))
{
profit_end(thepprofit);
profit_end(theqprofit);
thepprofit = profit_init(thepsf, MODEL_DIRAC);
theqprofit = profit_init(thepsf, MODEL_EXPONENTIAL);
}
}
#endif
}
/*-- Initialize PSF contexts and workspace */
if (prefs.psf_flag)
{
psf_readcontext(thepsf, field);
psf_init();
if (prefs.dpsf_flag)
{
psf_readcontext(thepsf, dfield);
psf_init();
}
}
/*-- Copy field structures to static ones (for catalog info) */
if (dfield)
{
thefield1 = *field;
thefield2 = *dfield;
}
else
thefield1 = thefield2 = *field;
if (wfield)
{
thewfield1 = *wfield;
thewfield2 = dwfield? *dwfield: *wfield;
}
else if (dwfield)
thewfield2 = *dwfield;
reinitcat(field);
/*-- Start the extraction pipeline */
NFPRINTF(OUTPUT, "Scanning image");
scanimage(field, dfield, pffield, prefs.nimaflag, wfield, dwfield,
dgeofield);
/*-- Finish the current CHECK-image processing */
if (prefs.check_flag)
for (i=0; i<MAXCHECK; i++)
if ((check=prefs.check[i]))
reendcheck(field, check);
/*-- Final time measurements*/
if (time(&thetime2)!=-1)
{
if (!strftime(thecat.ext_date, 12, "%d/%m/%Y", localtime(&thetime2)))
error(EXIT_FAILURE, "*Internal Error*: Date string too long ","");
if (!strftime(thecat.ext_time, 10, "%H:%M:%S", localtime(&thetime2)))
error(EXIT_FAILURE, "*Internal Error*: Time/date string too long ","");
thecat.ext_elapsed = difftime(thetime2, thetime1);
}
reendcat();
/* Update XML data */
if (prefs.xml_flag || prefs.cat_type==ASCII_VO)
update_xml(&thecat, dfield? dfield:field, field,
dwfield? dwfield:wfield, wfield);
/*-- Close ASSOC routines */
end_assoc(field);
for (i=0; i<prefs.nimaflag; i++)
endfield(pffield[i]);
endfield(field);
if (dfield)
endfield(dfield);
if (wfield)
endfield(wfield);
if (dwfield)
endfield(dwfield);
if (dgeofield)
endfield(dgeofield);
QPRINTF(OUTPUT, " Objects: detected %-8d / sextracted %-8d \n\n",
thecat.ndetect, thecat.ntotal);
}
if (nok<=0)
error(EXIT_FAILURE, "Not enough valid FITS image extensions in ",
prefs.image_name[0]);
free_cat(&imacat, 1);
NFPRINTF(OUTPUT, "Closing files");
/* End CHECK-image processing */
if (prefs.check_flag)
for (i=0; i<MAXCHECK; i++)
{
if ((check=prefs.check[i]))
endcheck(check);
prefs.check[i] = NULL;
}
if (prefs.filter_flag)
endfilter();
if (prefs.somfit_flag)
som_end(thesom);
if (prefs.growth_flag)
endgrowth();
#ifdef USE_MODEL
if (prefs.prof_flag)
{
profit_end(theprofit);
if (prefs.dprof_flag)
profit_end(thedprofit);
if (FLAG(obj2.prof_concentration)|FLAG(obj2.prof_concentration))
{
profit_end(thepprofit);
profit_end(theqprofit);
}
fft_end();
}
#endif
if (prefs.psf_flag)
psf_end(thepsf, thepsfit);
if (prefs.dpsf_flag)
psf_end(thedpsf, thedpsfit);
if (FLAG(obj2.sprob))
neurclose();
/* Processing end date and time */
thetimet2 = time(NULL);
tm = localtime(&thetimet2);
sprintf(prefs.sdate_end,"%04d-%02d-%02d",
tm->tm_year+1900, tm->tm_mon+1, tm->tm_mday);
sprintf(prefs.stime_end,"%02d:%02d:%02d",
tm->tm_hour, tm->tm_min, tm->tm_sec);
prefs.time_diff = counter_seconds() - dtime;
/* Write XML */
if (prefs.xml_flag)
write_xml(prefs.xml_name);
endcat((char *)NULL);
if (prefs.xml_flag || prefs.cat_type==ASCII_VO)
end_xml();
return;
}
/******************************** initglob ***********************************/
/*
Initialize a few global variables
*/
void initglob()
{
int i;
for (i=0; i<37; i++)
{
ctg[i] = cos(i*PI/18);
stg[i] = sin(i*PI/18);
}
return;
}
/****** selectext ************************************************************
PROTO int selectext(char *filename)
PURPOSE Return the user-selected extension number [%d] from the file name.
INPUT Filename character string.
OUTPUT Extension number, or RETURN_ERROR if nos extension specified.
NOTES The bracket and its extension number are removed from the filename if
found.
AUTHOR E. Bertin (IAP)
VERSION 08/10/2007
***/
static int selectext(char *filename)
{
char *bracl,*bracr;
int next;
if (filename && (bracl=strrchr(filename, '[')))
{
*bracl = '\0';
if ((bracr=strrchr(bracl+1, ']')))
*bracr = '\0';
next = strtol(bracl+1, NULL, 0);
return next;
}
return RETURN_ERROR;
}
/****** write_error ********************************************************
PROTO int write_error(char *msg1, char *msg2)
PURPOSE Manage files in case of a catched error
INPUT a character string,
another character string
OUTPUT RETURN_OK if everything went fine, RETURN_ERROR otherwise.
NOTES -.
AUTHOR E. Bertin (IAP)
VERSION 14/07/2006
***/
void write_error(char *msg1, char *msg2)
{
char error[MAXCHAR];
sprintf(error, "%s%s", msg1,msg2);
if (prefs.xml_flag)
write_xmlerror(prefs.xml_name, error);
/* Also close existing catalog */
endcat(error);
end_xml();
return;
}
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