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Unverified Commit 08c0ebe3 authored by Emmanuel Bertin's avatar Emmanuel Bertin Committed by GitHub
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Merge pull request #47 from astromatic/develop 

Develop
parents 9689a1c4 f7c10f46
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m4/acx_pthread.m4
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
dnl This file part of: AstrOmatic software
dnl
dnl Copyright: (C) 2002-2010 Emmanuel Bertin -- IAP/CNRS/UPMC
dnl Copyright: (C) 2002-2022 Emmanuel Bertin -- IAP/CNRS/SorbonneU
dnl (C) 2001 Steven G. Johnson (original version)
dnl
dnl Licenses: GPL (this version)
......@@ -25,7 +25,7 @@ dnl You should have received a copy of the GNU General Public License
dnl along with AstrOmatic software.
dnl If not, see <http://www.gnu.org/licenses/>.
dnl
dnl Last modified: 09/10/2010
dnl Last modified: 15/09/2022
dnl
dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
......@@ -88,7 +88,7 @@ if test x"$PTHREAD_LIBS$PTHREAD_CFLAGS" != x; then
save_LIBS="$LIBS"
LIBS="$PTHREAD_LIBS $LIBS"
AC_MSG_CHECKING([for pthread_join in LIBS=$PTHREAD_LIBS with CFLAGS=$PTHREAD_CFLAGS])
AC_TRY_LINK_FUNC(pthread_join, acx_pthread_ok=yes)
AC_LINK_IFELSE([AC_LANG_CALL([], pthread_join)], acx_pthread_ok=yes)
AC_MSG_RESULT($acx_pthread_ok)
if test x"$acx_pthread_ok" = xno; then
PTHREAD_LIBS=""
......@@ -170,10 +170,10 @@ for flag in $acx_pthread_flags; do
# pthread_cleanup_push because it is one of the few pthread
# functions on Solaris that doesn't have a non-functional libc stub.
# We try pthread_create on general principles.
AC_TRY_LINK([#include <pthread.h>],
AC_LINK_IFELSE([AC_LANG_CALL([#include <pthread.h>],
[pthread_t th; pthread_join(th, 0);
pthread_attr_init(0); pthread_cleanup_push(0, 0);
pthread_create(0,0,0,0); pthread_cleanup_pop(0); ],
pthread_create(0,0,0,0); pthread_cleanup_pop(0); ])],
[acx_pthread_ok=yes])
LIBS="$save_LIBS"
......@@ -199,12 +199,12 @@ if test "x$acx_pthread_ok" = xyes; then
# Detect AIX lossage: threads are created detached by default
# and the JOINABLE attribute has a nonstandard name (UNDETACHED).
AC_MSG_CHECKING([for joinable pthread attribute])
AC_TRY_LINK([#include <pthread.h>],
[int attr=PTHREAD_CREATE_JOINABLE;],
AC_LINK_IFELSE([AC_LANG_CALL([#include <pthread.h>],
[int attr=PTHREAD_CREATE_JOINABLE;])],
ok=PTHREAD_CREATE_JOINABLE, ok=unknown)
if test x"$ok" = xunknown; then
AC_TRY_LINK([#include <pthread.h>],
[int attr=PTHREAD_CREATE_UNDETACHED;],
AC_LINK_IFELSE([AC_LANG_CALL([#include <pthread.h>],
[int attr=PTHREAD_CREATE_UNDETACHED;])],
ok=PTHREAD_CREATE_UNDETACHED, ok=unknown)
fi
if test x"$ok" != xPTHREAD_CREATE_JOINABLE; then
......
sextractor.spec.in
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
#
# This file part of: SExtractor
#
# Copyright: (C) 2002-2020 IAP/CNRS/SorbonneU
# Copyright: (C) 2002-2022 IAP/CNRS/SorbonneU
#
# License: GNU General Public License
#
......@@ -22,7 +22,7 @@
# 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: 02/01/2020
# Last modified: 15/09/2022
#
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
......@@ -44,6 +44,7 @@ BuildRoot: %{_tmppath}/%{name}-buildroot
BuildRequires: pkgconfig
BuildRequires: fftw-devel >= 3.1
BuildRequires: atlas-devel >= 3.6.0
BuildRequires: cfitsio-devel >= 3.30
%description
Extract catalogs of sources from astronomical images
......
src/analyse.c
View file @ 08c0ebe3
......@@ -280,8 +280,7 @@ void examineiso(picstruct *field, picstruct *dfield, objstruct *obj,
emy2 /= flux2; /* variance of ym */
emxy /= flux2; /* covariance */
/*-- Handle fully correlated profile
s (which cause a singularity...) */
/*-- Handle fully correlated profiles (which cause a singularity...) */
esum *= 0.08333/flux2;
if (obj->singuflag && (emx2*emy2-emxy*emxy) < esum*esum)
{
......@@ -718,10 +717,10 @@ void endobject(picstruct *field, picstruct *dfield, picstruct *wfield,
dgeo_copy(dgeofield, outobj2.vignet_dgeox , outobj2.vignet_dgeoy,
prefs.vignet_dgeoxsize[0],prefs.vignet_dgeoxsize[1], ix,iy);
else {
if (FLAG(obj2.vignet_dgeox))
if (FLAG(obj2.vignet_dgeox))
dgeo_copy(dgeofield, outobj2.vignet_dgeox, NULL,
prefs.vignet_dgeoxsize[0],prefs.vignet_dgeoxsize[1], ix,iy);
if (FLAG(obj2.vignet_dgeoy))
if (FLAG(obj2.vignet_dgeoy))
dgeo_copy(dgeofield, NULL, outobj2.vignet_dgeoy,
prefs.vignet_dgeoysize[0],prefs.vignet_dgeoysize[1], ix,iy);
}
......
src/back.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2014 Emmanuel Bertin -- IAP/CNRS/UPMC
* Copyright: (C) 1993-2020 IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 17/06/2014
* Last modified: 23/09/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -52,8 +52,10 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
{
backstruct *backmesh,*wbackmesh, *bm,*wbm;
tabstruct *tab, *wtab;
PIXTYPE *buf,*wbuf, *buft,*wbuft;
OFF_T fcurpos,wfcurpos, wfcurpos2,fcurpos2, bufshift, jumpsize;
OFF_T2 fcurpos,wfcurpos, wfcurpos2,fcurpos2, bufshift, jumpsize;
OFF_T2 currentElement, wcurrentElement, currentElement2, wcurrentElement2;
size_t bufsize, bufsize2,
size,meshsize;
int i,j,k,m,n, step, nlines,
......@@ -65,7 +67,11 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
/* If the weight-map is not an external one, no stats are needed for it */
if (wfield && wfield->flags&(INTERP_FIELD|BACKRMS_FIELD))
wfield= NULL;
tab = field->tab;
if (wfield)
wtab = wfield->tab;
else
wtab = NULL; /* to avoid gcc -Wall warnings */
w = field->width;
bw = field->backw;
bh = field->backh;
......@@ -83,12 +89,20 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
wfcurpos = wfcurpos2 = 0; /* to avoid gcc -Wall warnings */
QFTELL(field->file, fcurpos, field->filename);
if (wfield)
#ifdef HAVE_CFITSIO
currentElement = (tab->currentElement == 0) ? 1 : tab->currentElement;
#endif
if (wfield) {
QFTELL(wfield->file, wfcurpos, wfield->filename);
#ifdef HAVE_CFITSIO
wcurrentElement = (wtab->currentElement == 0) ? 1 : wtab->currentElement;
#endif
}
/* Allocate a correct amount of memory to store pixels */
bufsize = (OFF_T)w*bh;
bufsize = (OFF_T2)w*bh;
meshsize = (size_t)bufsize;
nlines = 0;
if (bufsize > (size_t)BACK_BUFSIZE)
......@@ -96,8 +110,8 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
nlines = BACK_BUFSIZE/w;
step = (field->backh-1)/nlines+1;
bufsize = (size_t)(nlines = field->backh/step)*w;
bufshift = (step/2)*(OFF_T)w;
jumpsize = (step-1)*(OFF_T)w;
bufshift = (step/2)*(OFF_T2)w;
jumpsize = (step-1)*(OFF_T2)w;
}
else
bufshift = jumpsize = 0; /* to avoid gcc -Wall warnings */
......@@ -172,16 +186,23 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
{
/*---- Image size too big, we have to skip a few data !*/
QFTELL(field->file, fcurpos2, field->filename);
if (wfield)
#ifdef HAVE_CFITSIO
currentElement2 = (tab->currentElement == 0) ? 1 : tab->currentElement;
#endif
if (wfield){
QFTELL(wfield->file, wfcurpos2, wfield->filename);
#ifdef HAVE_CFITSIO
wcurrentElement2 = (wtab->currentElement == 0) ? 1 : wtab->currentElement;
#endif
}
if (j == ny-1 && (n=field->height%field->backh))
{
meshsize = n*(size_t)w;
nlines = BACK_BUFSIZE/w;
step = (n-1)/nlines+1;
bufsize = (nlines = n/step)*(size_t)w;
bufshift = (step/2)*(OFF_T)w;
jumpsize = (step-1)*(OFF_T)w;
bufshift = (step/2)*(OFF_T2)w;
jumpsize = (step-1)*(OFF_T2)w;
free(buf);
QMALLOC(buf, PIXTYPE, bufsize); /* pixel buffer */
if (wfield)
......@@ -192,35 +213,52 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
}
/*---- Read and skip, read and skip, etc... */
QFSEEK(field->file, bufshift*(OFF_T)field->bytepix, SEEK_CUR,
QFSEEK(field->file, bufshift*(OFF_T2)field->bytepix, SEEK_CUR,
field->filename);
#ifdef HAVE_CFITSIO
tab->currentElement += bufshift;
#endif
buft = buf;
for (i=nlines; i--; buft += w)
{
read_body(field->tab, buft, w);
if (i)
QFSEEK(field->file, jumpsize*(OFF_T)field->bytepix, SEEK_CUR,
if (i) {
QFSEEK(field->file, jumpsize*(OFF_T2)field->bytepix, SEEK_CUR,
field->filename);
#ifdef HAVE_CFITSIO
tab->currentElement += jumpsize;
#endif
}
}
if (wfield)
{
/*------ Read and skip, read and skip, etc... now on the weight-map */
QFSEEK(wfield->file, bufshift*(OFF_T)wfield->bytepix, SEEK_CUR,
QFSEEK(wfield->file, bufshift*(OFF_T2)wfield->bytepix, SEEK_CUR,
wfield->filename);
#ifdef HAVE_CFITSIO
wtab->currentElement += bufshift;
#endif
wbuft = wbuf;
for (i=nlines; i--; wbuft += w)
{
read_body(wfield->tab, wbuft, w);
weight_to_var(wfield, wbuft, w);
if (i)
QFSEEK(wfield->file, jumpsize*(OFF_T)wfield->bytepix, SEEK_CUR,
if (i){
QFSEEK(wfield->file, jumpsize*(OFF_T2)wfield->bytepix, SEEK_CUR,
wfield->filename);
#ifdef HAVE_CFITSIO
wtab->currentElement += jumpsize;
#endif
}
}
}
backstat(backmesh, wbackmesh, buf, wbuf, bufsize, nx, w, bw,
wfield?wfield->weight_thresh:0.0);
QFSEEK(field->file, fcurpos2, SEEK_SET, field->filename);
#ifdef HAVE_CFITSIO
tab->currentElement = currentElement2;
#endif
bm = backmesh;
for (m=nx; m--; bm++)
if (bm->mean <= -BIG)
......@@ -230,6 +268,9 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
if (wfield)
{
QFSEEK(wfield->file, wfcurpos2, SEEK_SET, wfield->filename);
#ifdef HAVE_CFITSIO
wtab->currentElement = wcurrentElement2;
#endif
wbm = wbackmesh;
for (m=nx; m--; wbm++)
if (wbm->mean <= -BIG)
......@@ -284,8 +325,15 @@ void makeback(picstruct *field, picstruct *wfield, int wscale_flag)
/* Go back to the original position */
QFSEEK(field->file, fcurpos, SEEK_SET, field->filename);
if (wfield)
#ifdef HAVE_CFITSIO
tab->currentElement = currentElement;
#endif
if (wfield) {
QFSEEK(wfield->file, wfcurpos, SEEK_SET, wfield->filename);
#ifdef HAVE_CFITSIO
wfield->tab->currentElement = wcurrentElement;
#endif
}
/* Median-filter and check suitability of the background map */
NFPRINTF(OUTPUT, "Filtering background map(s)");
......@@ -625,7 +673,7 @@ float backguess(backstruct *bkg, float *mean, float *sigma)
{
LONG *histo, *hilow, *hihigh, *histot;
unsigned long lowsum, highsum, sum;
double ftemp, mea, sig, sig1, med, dpix;
double ftemp, mea,meafac, sig, sig1, med,medfac, dpix;
int i, n, lcut,hcut, nlevelsm1, pix;
/* Leave here if the mesh is already classified as `bad' */
......@@ -641,6 +689,8 @@ float backguess(backstruct *bkg, float *mean, float *sigma)
sig = 10.0*nlevelsm1;
sig1 = 1.0;
medfac = prefs.back_pearson;
meafac = prefs.back_pearson - 1.0;
mea = med = bkg->mean;
for (n=100; n-- && (sig>=0.1) && (fabs(sig/sig1-1.0)>EPS);)
{
......@@ -677,7 +727,7 @@ float backguess(backstruct *bkg, float *mean, float *sigma)
*mean = fabs(sig)>0.0? (fabs(bkg->sigma/(sig*bkg->qscale)-1) < 0.0 ?
bkg->qzero+mea*bkg->qscale
:(fabs((mea-med)/sig)< 0.3 ?
bkg->qzero+(2.5*med-1.5*mea)*bkg->qscale
bkg->qzero+(medfac*med - meafac*mea)*bkg->qscale
:bkg->qzero+med*bkg->qscale))
:bkg->qzero+mea*bkg->qscale;
......
src/catout.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2020 IAP/CNRS/SorbonneU
* Copyright: (C) 1993-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 15/07/2020
* Last modified: 26/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -1059,7 +1059,7 @@ void reendcat()
{
keystruct *key;
tabstruct *tab;
OFF_T pos;
OFF_T2 pos;
char *head;
switch(prefs.cat_type)
......@@ -1086,6 +1086,7 @@ void reendcat()
QFTELL(fitscat->file, pos, fitscat->filename);
QFSEEK(fitscat->file, tab->headpos, SEEK_SET, fitscat->filename);
save_tab(fitscat, tab);
remove_tab(fitscat, "LDAC_IMHEAD", 0);
QFSEEK(fitscat->file, pos, SEEK_SET, fitscat->filename);
break;
......@@ -1127,4 +1128,3 @@ void zerocat(void)
}
src/check.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2013 Emmanuel Bertin -- IAP/CNRS/UPMC
* Copyright: (C) 1993-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 23/09/2013
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -406,6 +406,7 @@ void reinitcheck(picstruct *field, checkstruct *check)
remove_tabs(cat);
copy_tab_fromptr(field->tab, cat, 0);
tab = cat->tab;
decomp_head(tab);
tab->cat = cat;
if (check->next<=1)
prim_head(tab);
......
src/define.h
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2015 Emmanuel Bertin -- IAP/CNRS/UPMC
* Copyright: (C) 1993-2022 Emmanuel Bertin -- IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 11/03/2015
* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -167,7 +167,7 @@
#define QCALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)calloc((size_t)(nel),sizeof(typ)))) \
{ \
sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
......@@ -177,7 +177,7 @@
#define QMALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)malloc((size_t)(nel)*sizeof(typ)))) \
{ \
sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
......@@ -187,7 +187,7 @@
#define QMALLOC16(ptr, typ, nel) \
{if (posix_memalign((void **)&ptr, 16, (size_t)(nel)*sizeof(typ))) \
{ \
sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
......@@ -197,7 +197,7 @@
#define QREALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)realloc(ptr, (size_t)(nel)*sizeof(typ))))\
{ \
sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
......@@ -208,7 +208,7 @@
{if (ptrin) \
{if (!(ptrout = (typ *)malloc((size_t)(nel)*sizeof(typ)))) \
{ \
sprintf(gstr, #ptrout " (" #nel "=%lld elements) " \
sprintf(gstr, #ptrout " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE,"Could not allocate memory for ",gstr);\
......
src/fft.h
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 2007-2017 IAP/CNRS/UPMC
* Copyright: (C) 2007-2022 IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 19/06/2017
* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -40,7 +40,7 @@
#define QFFTWF_MALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)fftwf_malloc((size_t)(nel)*sizeof(typ)))) \
{ \
sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
......
src/field.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2012 Emmanuel Bertin -- IAP/CNRS/UPMC
* Copyright: (C) 1993-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 12/07/2012
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -70,21 +70,41 @@ picstruct *newfield(char *filename, int flags, int ext)
field->cat = cat;
nok = 0;
tab = cat->tab;
#ifdef HAVE_CFITSIO
if ((tab->isTileCompressed) ||
(tab->naxis >= 2
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8)))
#else
if (tab->isTileCompressed)
warning(BANNER " has been compiled without CFITSIO support: "
"compressed image skipped in ", filename);
if (tab->naxis >= 2
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8))
#endif
nok++;
ext2 = ext;
for (ntab=cat->ntab; ext2-- && ntab--;)
{
tab=tab->nexttab;
#ifdef HAVE_CFITSIO
if ((tab->isTileCompressed) ||
(tab->naxis >= 2
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8)))
#else
if (tab->isTileCompressed)
warning(BANNER " has been compiled without CFITSIO support: "
"compressed image skipped in ", filename);
if (tab->naxis >= 2
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8))
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8))
#endif
nok++;
}
if (!nok)
error(EXIT_FAILURE, "Not a valid FITS image in ",filename);
error(EXIT_FAILURE, "Not a valid FITS image in ", filename);
field->tab = tab;
if (ntab<0)
......
src/fits/fitsbody.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
* Copyright: (C) 1995-2010 IAP/CNRS/SorbonneU
* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/02/2020
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -43,6 +43,10 @@
#include "fitscat_defs.h"
#include "fitscat.h"
#ifdef HAVE_CFITSIO
#include CFITSIO_H
#endif
size_t body_maxram = BODY_DEFRAM,
body_maxvram = BODY_DEFVRAM,
body_ramleft, body_vramleft, body_ramflag;
......@@ -60,7 +64,7 @@ INPUT Table (tab) structure.
OUTPUT Pointer to the mapped data if OK, or NULL otherwise.
NOTES The file pointer must be positioned at the beginning of the data.
AUTHOR E. Bertin (IAP)
VERSION 05/05/2001
VERSION 02/10/2017
***/
PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
{
......@@ -85,7 +89,11 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
tab->extname);
/* Decide if the data will go in physical memory or on swap-space */
#ifdef HAVE_CFITSIO
npix = tab->naxisn[0] * tab->naxisn[1];
#else
npix = tab->tabsize/tab->bytepix;
#endif
size = npix*sizeof(PIXTYPE);
if (size < body_ramleft)
{
......@@ -93,6 +101,9 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
if ((tab->bodybuf = malloc(size)))
{
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
#ifdef HAVE_CFITSIO
tab->currentElement = 1;
#endif
read_body(tab, (PIXTYPE *)tab->bodybuf, npix);
/*---- Apply pixel processing */
if (func)
......@@ -120,6 +131,9 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
if (!spoonful)
spoonful = DATA_BUFSIZE;
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
#ifdef HAVE_CFITSIO
tab->currentElement = 1;
#endif
read_body(tab, buffer, spoonful/sizeof(PIXTYPE));
/*-- Apply pixel processing */
if (func)
......@@ -159,7 +173,7 @@ INPUT Table (tab) structure.
OUTPUT Pointer to the mapped data if OK, or NULL otherwise.
NOTES The file pointer must be positioned at the beginning of the data.
AUTHOR E. Bertin (IAP)
VERSION 30/01/2012
VERSION 02/10/2017
***/
FLAGTYPE *alloc_ibody(tabstruct *tab,
void (*func)(FLAGTYPE *ptr, int npix))
......@@ -193,6 +207,9 @@ FLAGTYPE *alloc_ibody(tabstruct *tab,
if ((tab->bodybuf = malloc(size)))
{
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
#ifdef HAVE_CFITSIO
tab->currentElement = 1;
#endif
read_ibody(tab, (FLAGTYPE *)tab->bodybuf, npix);
/*---- Apply pixel processing */
if (func)
......@@ -220,6 +237,9 @@ FLAGTYPE *alloc_ibody(tabstruct *tab,
if (!spoonful)
spoonful = DATA_BUFSIZE;
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
#ifdef HAVE_CFITSIO
tab->currentElement = 1;
#endif
read_ibody(tab, buffer, spoonful/sizeof(FLAGTYPE));
/*-- Apply pixel processing */
if (func)
......@@ -294,6 +314,77 @@ void free_body(tabstruct *tab)
return;
}
#ifdef HAVE_CFITSIO
/******* readTileCompressed ***************************************************
*
* Function to read a chunk of a tile-compressed FITS image
*
***/
void readTileCompressed(tabstruct *tab, size_t spoonful, void *bufdata0) {
int status, hdutype;
// first of all, move to correct HDU
status = 0;
fits_movabs_hdu(tab->infptr, tab->hdunum, &hdutype, &status);
if (status != 0) {
printf("Error moving to HDU %d\n", tab->hdunum);
fits_report_error(stderr, status);
}
// pixels count from 1
if (!tab->currentElement)
tab->currentElement = 1;
// now read section of image
int datatype;
switch(tab->bitpix){
case BYTE_IMG:
datatype = TBYTE;
break;
case SHORT_IMG:
datatype = TSHORT;
break;
case LONG_IMG:
datatype = TLONG;
break;
case FLOAT_IMG:
datatype = TFLOAT;
break;
case DOUBLE_IMG:
datatype = TDOUBLE;
break;
default:
datatype = TFLOAT;
break;
}
int anynul;
double bscale = 1.0, bzero = 0.0, nulval = 0.;
// turn off any scaling so that we copy raw pixel values
status = 0;
fits_set_bscale(tab->infptr, bscale, bzero, &status);
// now read the image
status = 0;
fits_read_img(tab->infptr, datatype, tab->currentElement, spoonful, &nulval,
bufdata0, &anynul, &status);
// report reading error
if (status) {
printf("CFITSIO ERROR reading start=%d end=%d absolute end=%d\n",
tab->currentElement,
(tab->currentElement + spoonful),
(tab->naxisn[0]*tab->naxisn[1]));
fits_report_error(stderr, status);
}
// update file 'pointer'
tab->currentElement += spoonful;
}
#endif // HAVE_CFITSIO
/******* read_body ************************************************************
PROTO read_body(tabstruct *tab, PIXTYPE *ptr, long size)
......@@ -303,8 +394,8 @@ INPUT A pointer to the tab structure,
the number of elements to be read.
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
VERSION 11/02/2020
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
{
......@@ -323,15 +414,15 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
int curval, dval, blankflag, bswapflag, ival, iblank;
size_t i, bowl, spoonful, npix;
PIXTYPE bs,bz;
double bs,bz;
/* a NULL cat structure indicates that no data can be read */
if (!(cat = tab->cat))
return;
bs = (PIXTYPE)tab->bscale;
bz = (PIXTYPE)tab->bzero;
bs = tab->bscale;
bz = tab->bzero;
blankflag = tab->blankflag;
bswapflag = *((char *)&ashort); // Byte-swapping flag
......@@ -346,7 +437,15 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
if (spoonful>size)
spoonful = size;
bufdata = (char *)bufdata0;
#ifdef HAVE_CFITSIO
if (tab->isTileCompressed && tab->infptr)
readTileCompressed(tab, spoonful, (void *)bufdata0);
else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
#else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
#endif // HAVE_CFITSIO
switch(tab->bitpix)
{
case BP_BYTE:
......@@ -383,7 +482,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
case BP_SHORT:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 2, spoonful);
if (blankflag)
{
......@@ -418,7 +521,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
case BP_LONG:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 4, spoonful);
if (blankflag)
{
......@@ -454,7 +561,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
#ifdef HAVE_LONG_LONG_INT
case BP_LONGLONG:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 8, spoonful);
if (blankflag)
{
......@@ -489,7 +600,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
#endif
case BP_FLOAT:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 4, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(float))
......@@ -499,7 +614,12 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
case BP_DOUBLE:
if (bswapflag)
{
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed)
swapbytes(bufdata, 8, spoonful);
#else
swapbytes(bufdata, 8, spoonful);
#endif
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(double))
*(ptr++) = ((0x7ff00000 & *(unsigned int *)(bufdata+4))
......@@ -632,7 +752,7 @@ INPUT A pointer to the tab structure,
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
VERSION 11/02/2020
VERSION 26/08/2020
***/
void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
{
......@@ -660,7 +780,15 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
if (spoonful>size)
spoonful = size;
bufdata = (char *)bufdata0;
#ifdef HAVE_CFITSIO
if (tab->isTileCompressed)
readTileCompressed(tab, spoonful, (void *)bufdata0);
else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
#else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
#endif
switch(tab->bitpix)
{
case BP_BYTE:
......@@ -670,7 +798,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
break;
case BP_SHORT:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 2, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(unsigned short))
......@@ -678,7 +810,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
break;
case BP_LONG:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 4, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(unsigned int))
......@@ -687,7 +823,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
#ifdef HAVE_LONG_LONG_INT
case BP_LONGLONG:
#ifdef HAVE_CFITSIO
if (!tab->isTileCompressed && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(bufdata, 8, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(ULONGLONG))
......@@ -815,7 +955,7 @@ INPUT A pointer to the tab structure,
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
VERSION 11/02/2020
VERSION 26/08/2020
***/
void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
{
......@@ -931,7 +1071,12 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
#pragma ivdep
for (i=spoonful; i--;)
*(bufdata++) = (*(ptr++)-bz)/bs;
#ifdef HAVE_CFITSIO
if (!tab->infptr && bswapflag)
#else
if (bswapflag)
#endif
swapbytes(cbufdata0, 4, spoonful);
}
break;
......@@ -952,7 +1097,61 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
"read_body()");
break;
}
#ifdef HAVE_CFITSIO
// if cfitsio output file has been set up, then proceed to write
if (tab->infptr) {
// now read section of image
int datatype;
switch(tab->bitpix) {
case BYTE_IMG:
datatype = TBYTE;
break;
case SHORT_IMG:
datatype = TSHORT;
break;
case LONG_IMG:
datatype = TLONG;
break;
case FLOAT_IMG:
datatype = TFLOAT;
break;
case DOUBLE_IMG:
datatype = TDOUBLE;
break;
default:
datatype = TFLOAT;
break;
}
// turn off any scaling so that we copy the raw pixel values
double *array,
bscale = 1.0,
bzero = 0.0,
nulval = 0.0;
int status = 0;
fits_set_bscale(tab->infptr, bscale, bzero, &status);
status = 0;
fits_write_img(tab->infptr, datatype, tab->currentElement, spoonful,
cbufdata0, &status);
if (status) {
printf("CFITSIO ERROR writing start=%d end=%d absolute end=%d\n",
tab->currentElement, (tab->currentElement + spoonful),
(tab->naxisn[0]*tab->naxisn[1]));
fits_report_error(stderr, status);
}
tab->currentElement = tab->currentElement + spoonful;
} else
// otherwise, continue with usual AstrOmatic fits writing routine
QFWRITE(cbufdata0, spoonful*tab->bytepix, cat->file, cat->filename);
#else
QFWRITE(cbufdata0, spoonful*tab->bytepix, cat->file, cat->filename);
#endif // HAVE_CFITSIO
}
break;
......
src/fits/fitscat.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
* Copyright: (C) 1995-2020 IAP/CNRS/SorbonneU
* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 15/07/2020
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -42,6 +42,8 @@
#include "fitscat_defs.h"
#include "fitscat.h"
extern float *fits_rand_value;
char fits_str[MAXCHAR];
/****** about_cat **************************************************************
......@@ -167,6 +169,37 @@ int close_cat(catstruct *cat)
return RETURN_OK;
}
#ifdef HAVE_CFITSIO
/****** close_cfitsio **********************************************************
PROTO int close_cfitsio(fitsfile **infptr)
PURPOSE Close a file previously opened by cfitsio
INPUT fitsfile structure.
OUTPUT RETURN_OK if everything went as expected (exit in error otherwise).
NOTES the fitsfile pointer is set to NULL;
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
int close_cfitsio(catstruct *cat) {
if ((cat) && (cat->infptr)) {
int status = 0; fits_close_file(cat->infptr, &status);
if (status != 0) {
fits_report_error(stderr, status);
error(EXIT_FAILURE, "Could not close FITS file with cfitsio: ",
cat->filename);
} else {
// Successfully closed FITS file with cfitsio
cat->infptr == NULL;
// Free random seed in CFITSIO.
QFREE(fits_rand_value);
}
} else
return RETURN_ERROR;
return RETURN_OK;
}
#endif // HAVE_CFITSIO
/****** free_cat ***************************************************************
PROTO void free_cat(catstruct **cat, int ncat)
......@@ -175,8 +208,8 @@ INPUT Pointer to a catalog structure,
Number of catalogs.
OUTPUT -.
NOTES Unallocated pointers should have been put to NULL.
AUTHOR E. Bertin (IAP & Leiden observatory)
VERSION 05/12/2009
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
void free_cat(catstruct **cat, int ncat)
......@@ -191,6 +224,10 @@ void free_cat(catstruct **cat, int ncat)
if ((*thecat)->file)
close_cat(*thecat);
remove_tabs(*thecat);
#ifdef HAVE_CFITSIO
// Free resources allocated for CFITSIO
close_cfitsio(*thecat);
#endif
free(*(thecat++));
}
......@@ -311,8 +348,8 @@ PURPOSE Explores the whole FITS file
INPUT catalog structure.
OUTPUT RETURN_OK if at least one table was found, RETURN_ERROR otherwise.
NOTES Memory space for the array of fits structures is reallocated.
AUTHOR E. Bertin (IAP & Leiden observatory)
VERSION 14/12/2002
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
int map_cat(catstruct *cat)
......@@ -325,14 +362,38 @@ int map_cat(catstruct *cat)
QCALLOC(tab, tabstruct, 1);
tab->cat = cat;
QFTELL(cat->file, tab->headpos, cat->filename);
#ifdef HAVE_CFITSIO
fitsfile *infptr;
int status, hdutype, hdunum = 1;
#endif // HAVE_CFITSIO
for (ntab=0; !get_head(tab); ntab++)
{
readbasic_head(tab);
readbintabparam_head(tab);
QFTELL(cat->file, tab->bodypos, cat->filename);
tab->nseg = tab->seg = 1;
#ifdef HAVE_CFITSIO
if (tab->isTileCompressed) {
// Trigger CFITSIO file opening
status = 0;
if (!cat->infptr) {
fits_open_file(&cat->infptr, cat->filename, READONLY, &status);
if (status != 0) {
fits_report_error(stderr, status);
error(EXIT_FAILURE,
"Could not open FITS file with cfitsio: %s\n", cat->filename);
}
}
tab->infptr = cat->infptr;
}
tab->hdunum = hdunum++;
#endif // HAVE_CFITSIO
if (tab->tabsize)
QFSEEK(cat->file, PADTOTAL(tab->tabsize), SEEK_CUR, cat->filename);
if (prevtab)
{
tab->prevtab = prevtab;
......
src/fits/fitscat.h
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
* Copyright: (C) 1995-2020 IAP/CNRS/SorbonneU
* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/02/2020
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -36,6 +36,10 @@
#include <sys/types.h>
#endif
#ifdef HAVE_CFITSIO
#include CFITSIO_H
#endif
#define MAXCHARS 256 /* max. number of characters */
#define WARNING_NMAX 1000 /* max. number of recorded warnings */
......@@ -107,10 +111,11 @@ typedef long long SLONGLONG;
typedef union {int l[2];} SLONGLONG;
#endif
#if defined(_FILE_OFFSET_BITS) && !defined(OFF_T)
#define OFF_T off_t
// CFITSIO changed OFF_T to OFF_T2 due to clash with cfitsio lib
#if defined(_FILE_OFFSET_BITS) && !defined(OFF_T2)
#define OFF_T2 off_t
#else
#define OFF_T long
#define OFF_T2 long
#endif
/*------------------------------- constants ---------------------------------*/
......@@ -150,6 +155,9 @@ typedef struct structcat
struct structtab *tab; /* pointer to the first table */
int ntab; /* number of tables included */
access_type_t access_type; /* READ_ONLY or WRITE_ONLY */
#ifdef HAVE_CFITSIO
fitsfile *infptr; /* a cfitsio pointer to the file */
#endif
} catstruct;
/*-------------------------------- table ----------------------------------*/
......@@ -180,8 +188,8 @@ typedef struct structtab
char *headbuf; /* buffer containing the header */
int headnblock; /* number of FITS blocks */
char *bodybuf; /* buffer containing the body */
OFF_T bodypos; /* position of the body in the file */
OFF_T headpos; /* position of the head in the file */
OFF_T2 bodypos; /* position of the body in the file */
OFF_T2 headpos; /* position of the head in the file */
struct structcat *cat; /* (original) parent catalog */
struct structtab *prevtab, *nexttab; /* previous and next tab in chain */
int seg; /* segment position */
......@@ -190,7 +198,13 @@ typedef struct structtab
int nkey; /* number of keys */
int swapflag; /* mapped to a swap file ? */
char swapname[MAXCHARS]; /* name of the swapfile */
unsigned int bodysum; /* Checksum of the FITS body */
unsigned int bodysum; /* Checksum of the FITS body */
int isTileCompressed; /* is this a tile compressed image? */
#ifdef HAVE_CFITSIO
fitsfile *infptr; /* a cfitsio pointer to the file */
int hdunum; /* FITS HDU number for this 'table' */
long currentElement; /* tracks the current image pixel */
#endif
} tabstruct;
......@@ -218,8 +232,8 @@ extern void add_cleanupfilename(char *filename),
encode_checksum(unsigned int sum, char *str),
end_readobj(tabstruct *keytab, tabstruct *tab, char *buf),
end_writeobj(catstruct *cat, tabstruct *tab, char *buf),
error(int, char *, char *),
error_installfunc(void (*func)(char *msg1, char *msg2)),
error(int code, const char *msg1, const char *msg2),
error_installfunc(void (*func)(const char *msg1, const char *msg2)),
fixexponent(char *s),
free_body(tabstruct *tab),
free_cat(catstruct **cat, int ncat),
......@@ -271,6 +285,9 @@ extern int about_cat(catstruct *cat, FILE *stream),
add_tab(tabstruct *tab, catstruct *cat, int pos),
blank_keys(tabstruct *tab),
close_cat(catstruct *cat),
#ifdef HAVE_CFITSIO
close_cfitsio(catstruct *cat),
#endif
copy_key(tabstruct *tabin, char *keyname, tabstruct *tabout,
int pos),
copy_tab(catstruct *catin, char *tabname, int seg,
......@@ -315,6 +332,7 @@ extern int about_cat(catstruct *cat, FILE *stream),
tformof(char *str, t_type ttype, int n),
tsizeof(char *str),
update_head(tabstruct *tab),
decomp_head(tabstruct *tab),
update_tab(tabstruct *tab),
verify_checksum(tabstruct *tab),
write_obj(tabstruct *tab, char *buf),
......@@ -328,8 +346,4 @@ extern FLAGTYPE *alloc_ibody(tabstruct *tab,
extern t_type ttypeof(char *str);
extern void error(int, char *, char *),
swapbytes(void *ptr, int nb, int n),
warning(char *msg1, char *msg2);
#endif
src/fits/fitshead.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
* Copyright: (C) 1995-2022 IAP/CNRS/SorbonneU
* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/03/2022
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -100,64 +100,92 @@ PURPOSE Read the current FITS header basic keywords.
INPUT pointer to catstruct.
OUTPUT -.
NOTES -.
AUTHOR E. Bertin (IAP)
VERSION 03/06/2012
AUTHOR E. Bertin (CFHT/IAP/SorbonneU)
VERSION 25/02/2023
***/
void readbasic_head(tabstruct *tab)
{
char str[88];
char key[12], name[16],
*filename;
int i;
*bitpix_key, *naxis_key, *filename;
int i, bitpix, bytepix, naxis, naxisn;
KINGSIZE_T tabsize;
filename = (tab->cat? tab->cat->filename : strcpy(name, "internal header"));
if (fitsread(tab->headbuf, "BITPIX ", &tab->bitpix, H_INT, T_LONG)
==RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
tab->isTileCompressed = (fitsread(tab->headbuf, "ZIMAGE ",
str, H_STRING, T_STRING) == RETURN_OK)? 1 : 0;
tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
if (fitsread(tab->headbuf, tab->isTileCompressed ? "ZBITPIX " : "BITPIX ",
&tab->bitpix, H_INT, T_LONG) == RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
if (fitsread(tab->headbuf, "NAXIS ", &tab->naxis, H_INT, T_LONG)
==RETURN_ERROR)
if (fitsread(tab->headbuf, tab->isTileCompressed ? "ZNAXIS " : "NAXIS ",
&tab->naxis, H_INT, T_LONG) == RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
tabsize = 0;
if (tab->naxis>0)
{
tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
if (tab->naxis>0) {
QFREE(tab->naxisn);
QMALLOC(tab->naxisn, int, tab->naxis);
/*--get the size of the array*/
tabsize = 1;
for (i=0; i<tab->naxis && i<999; i++)
{
sprintf(key,"NAXIS%-3d", i+1);
for (i=0; i<tab->naxis && i<999; i++) {
sprintf(key, tab->isTileCompressed? "ZNAXIS%-2d" : "NAXIS%-3d", i+1);
if (fitsread(tab->headbuf, key, &tab->naxisn[i], H_INT, T_LONG)
==RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: incoherent FITS header in ", filename);
tabsize *= tab->naxisn[i];
}
error(EXIT_FAILURE, "*Error*: inconsistent FITS header in ", filename);
}
}
/*random groups parameters (optional)*/
tab->pcount = 0;
fitsread(tab->headbuf, "PCOUNT ", &tab->pcount, H_INT, T_LONG);
tab->gcount = 1;
fitsread(tab->headbuf, "GCOUNT ", &tab->gcount, H_INT, T_LONG);
/*number of fields (only for tables)*/
tab->tfields = 0;
fitsread(tab->headbuf, "TFIELDS ", &tab->tfields, H_INT, T_LONG);
/*in case of a non-primary header*/
/* In case of a non-primary header*/
tab->xtension[0] = (char)'\0';
fitsread(tab->headbuf, "XTENSION", tab->xtension, H_STRING, T_STRING);
tab->extname[0] = (char)'\0';
fitsread(tab->headbuf, "EXTNAME ", tab->extname, H_STRING, T_STRING);
tab->tabsize = tab->bytepix*tab->gcount*((size_t)tab->pcount+tabsize);
/* Number of fields (only for tables)*/
tab->tfields = 0;
fitsread(tab->headbuf, "TFIELDS ", &tab->tfields, H_INT, T_LONG);
/* Random groups parameters (optional)*/
tab->gcount = 1;
fitsread(tab->headbuf, "GCOUNT ", &tab->gcount, H_INT, T_LONG);
tab->pcount = 0;
fitsread(tab->headbuf, "PCOUNT ", &tab->pcount, H_INT, T_LONG);
/* Compute extension body size in bytes */
if (tab->isTileCompressed) {
if (fitsread(tab->headbuf, "BITPIX ",
&bitpix, H_INT, T_LONG) == RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
bytepix = bitpix>0?(bitpix/8):(-bitpix/8);
if (fitsread(tab->headbuf, "NAXIS ", &naxis, H_INT, T_LONG)
==RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
if ((naxis)) {
tabsize = 1;
for (i=0; i<naxis && i<999; i++) {
naxisn = 1;
sprintf(key,"NAXIS%-3d", i+1);
if (fitsread(tab->headbuf, key, &naxisn, H_INT, T_LONG)
==RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: inconsistent FITS header in ", filename);
tabsize *= naxisn;
}
} else
tabsize = 0;
} else {
bytepix = tab->bytepix;
if ((tab->naxis)) {
tabsize = 1;
for (i=0; i<tab->naxis && i<999; i++)
tabsize *= tab->naxisn[i];
} else
tabsize = 0;
}
tab->tabsize = bytepix*tab->gcount*((size_t)tab->pcount+tabsize);
/* Scaling parameters for basic FITS integer arrays */
tab->bscale = 1.0;
......@@ -284,7 +312,12 @@ int readbintabparam_head(tabstruct *tab)
key->htype = H_STRING;
break;
default:
#ifdef HAVE_CFITSIO
// CFITSIO TODO dodgy
key->ttype = T_FLOAT;
#else
error(EXIT_FAILURE, "*Error*: Unknown TFORM in ", cat->filename);
#endif
}
/*--handle the special case of multimensional arrays*/
......@@ -893,3 +926,49 @@ char *printftotdisp(char *cprintf, char *str)
return str;
}
/****** decomp_head ***********************************************************
PROTO int decomp_head(tabstruct *tab)
PURPOSE Update a FITS header so that it now matches uncompressed data format.
INPUT Table structure.
OUTPUT RETURN_OK if tab is a compressed binary table,
or RETURN_ERROR otherwise.
NOTES The headbuf pointer in the tabstruct might be reallocated.
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
int decomp_head(tabstruct *tab) {
#ifdef HAVE_CFITSIO
/* Update XTENSION, the extension type */
if (tab->isTileCompressed && *tab->xtension) {
strcpy(tab->xtension, "IMAGE");
addkeywordto_head(tab, "XTENSION", "EXTENSION TYPE");
fitswrite(tab->headbuf, "XTENSION", tab->xtension, H_STRING, T_STRING);
addkeywordto_head(tab, "PCOUNT ", "required keyword; must = 0");
addkeywordto_head(tab, "GCOUNT ", "required keyword; must = 1");
tab->pcount = 0;
tab->gcount = 1;
fitswrite(tab->headbuf,"PCOUNT ", &tab->pcount, H_INT, T_LONG);
fitswrite(tab->headbuf,"GCOUNT ", &tab->gcount, H_INT, T_LONG);
tab->isTileCompressed = 0;
/*-- Remove all compression-related keywords */
removekeywordfrom_head(tab, "TFIELDS?");
removekeywordfrom_head(tab, "TTYPE???");
removekeywordfrom_head(tab, "TFORM???");
removekeywordfrom_head(tab, "ZIMAGE??");
removekeywordfrom_head(tab, "ZBITPIX?");
removekeywordfrom_head(tab, "ZNAXIS??");
removekeywordfrom_head(tab, "ZTILE???");
removekeywordfrom_head(tab, "ZCMPTYPE");
removekeywordfrom_head(tab, "ZNAME???");
removekeywordfrom_head(tab, "ZVAL????");
update_head(tab);
return RETURN_OK;
} else
#endif
return RETURN_ERROR;
}
src/fits/fitskey.c
View file @ 08c0ebe3
......@@ -991,7 +991,7 @@ void show_keys(tabstruct *tab, char **keynames, keystruct **keys, int nkeys,
if (kflag)
free(keys);
if (o_type == SHOW_SKYCAT)
fprintf(stream, skycattail, 1.0);
fprintf(stream, "%s", skycattail);
return;
}
src/fits/fitsmisc.c
View file @ 08c0ebe3
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 09/10/2010
* Last modified: 20/11/2013
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -40,7 +40,7 @@
#include "fitscat_defs.h"
#include "fitscat.h"
static void (*errorfunc)(char *msg1, char *msg2) = NULL;
static void (*errorfunc)(const char *msg1, const char *msg2) = NULL;
static char warning_historystr[WARNING_NMAX][192]={""};
static int nwarning = 0, nwarning_history = 0, nerror = 0;
......@@ -48,7 +48,7 @@ static int nwarning = 0, nwarning_history = 0, nerror = 0;
/*
I hope it will never be used!
*/
void error(int num, char *msg1, char *msg2)
void error(int num, const char *msg1, const char *msg2)
{
fprintf(stderr, "\n> %s%s\n\n",msg1,msg2);
if (num && errorfunc && !nerror)
......@@ -64,7 +64,7 @@ void error(int num, char *msg1, char *msg2)
/*
I hope it will never be used!
*/
void error_installfunc(void (*func)(char *msg1, char *msg2))
void error_installfunc(void (*func)(const char *msg1, const char *msg2))
{
if (func)
errorfunc = func;
......
src/fits/fitstab.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
* Copyright: (C) 1995-2010 Emmanuel Bertin -- IAP/CNRS/UPMC
* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/09/2012
* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -35,6 +35,10 @@
#include <stdlib.h>
#include <string.h>
#ifdef HAVE_CFITSIO
#include CFITSIO_H
#endif
#include "fitscat_defs.h"
#include "fitscat.h"
......@@ -270,8 +274,8 @@ INPUT Pointer to the original catalog,
Position (1= first after the primary HDU, <=0 = at the end)
OUTPUT -.
NOTES -.
AUTHOR E. Bertin (IAP & Leiden observatory)
VERSION 22/06/2001
AUTHOR E. Bertin (IAP/SorbonneU)
VERSION 25/02/2023
***/
void copy_tab_fromptr(tabstruct *tabin, catstruct *catout, int pos)
......@@ -318,6 +322,11 @@ void copy_tab_fromptr(tabstruct *tabin, catstruct *catout, int pos)
prevtab->nexttab = nexttab;
nexttab->prevtab = prevtab;
#ifdef HAVE_CFITSIO
// Do not copy CFitsIO file pointer
tabout->infptr = NULL;
#endif
return;
}
......@@ -396,8 +405,8 @@ PURPOSE Free memory associated to a table pointer.
INPUT Pointer to the table.
OUTPUT -.
NOTES -.
AUTHOR E. Bertin (IAP & Leiden observatory)
VERSION 28/02/2000
AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
VERSION 25/02/2023
***/
void free_tab(tabstruct *tab)
......
src/fits/fitswrite.c
View file @ 08c0ebe3
......@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see <http://www.gnu.org/licenses/>.
*
* Last modified: 11/02/2020
* Last modified: 26/08/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -359,13 +359,13 @@ INPUT catalog structure,
OUTPUT -.
NOTES -.
AUTHOR E. Bertin (IAP & Leiden observatory)
VERSION 26/09/2004
VERSION 03/12/2019
***/
void end_writeobj(catstruct *cat, tabstruct *tab, char *buf)
{
keystruct *key;
OFF_T pos;
OFF_T2 pos;
int k;
/* Make the table parameters reflect its content*/
......
src/globals.h
View file @ 08c0ebe3
......@@ -22,7 +22,7 @@
* 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: 15/07/2020
* Last modified: 23/09/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -82,7 +82,7 @@ extern void alloccatparams(void),
updateparamflags(void),
useprefs(void),
writecat(int, objliststruct *),
write_error(char *msg1, char *msg2),
write_error(const char *msg1, const char *msg2),
write_vo_fields(FILE *file),
zerocat(void);
......
src/header.c
View file @ 08c0ebe3
......@@ -22,7 +22,7 @@
* 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: 12/07/2012
* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -49,7 +49,7 @@ INPUT Name of the ASCII file,
OUTPUT RETURN_OK if the file was found, RETURN_ERROR otherwise.
NOTES -.
AUTHOR E. Bertin (IAP)
VERSION 12/07/2012
VERSION 07/09/2022
***/
int read_aschead(char *filename, int frameno, tabstruct *tab)
{
......@@ -63,7 +63,7 @@ int read_aschead(char *filename, int frameno, tabstruct *tab)
{
/*- Skip previous ENDs in multi-FITS extension headers */
for (i=frameno-1; i--;)
while (fgets(str, MAXCHAR, file)
while (fgets(str, 88, file)
&& strncmp(str,"END ",4)
&& strncmp(str,"END\n",4));
memset(str, ' ', 80);
......
src/makeit.c
View file @ 08c0ebe3
......@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
* Copyright: (C) 1993-2020 IAP/CNRS/SorbonneU
* Copyright: (C) 1993-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
......@@ -22,7 +22,7 @@
* 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: 15/07/2020
* Last modified: 07/03/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
......@@ -43,7 +43,9 @@
#include "assoc.h"
#include "back.h"
#include "check.h"
#ifdef USE_MODEL
#include "fft.h"
#endif
#include "field.h"
#include "filter.h"
#include "growth.h"
......@@ -280,7 +282,7 @@ void makeit()
{
/*---- Check for the next valid image extension */
if ((imatab->naxis < 2)
|| !strncmp(imatab->xtension, "BINTABLE", 8)
|| !(imatab->isTileCompressed || strncmp(imatab->xtension, "BINTABLE", 8))
|| !strncmp(imatab->xtension, "ASCTABLE", 8))
continue;
next++;
......@@ -319,10 +321,9 @@ void makeit()
{
/*-- Check for the next valid image extension */
if (!forcextflag && ((imatab->naxis < 2)
|| !strncmp(imatab->xtension, "BINTABLE", 8)
|| !(imatab->isTileCompressed || strncmp(imatab->xtension, "BINTABLE", 8))
|| !strncmp(imatab->xtension, "ASCTABLE", 8)))
continue;
nok++;
/*-- Initial time measurement*/
......@@ -706,8 +707,8 @@ 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
AUTHOR E. Bertin (CFHT/IAP)
VERSION 07/03/2023
***/
static int selectext(char *filename)
{
......@@ -720,6 +721,7 @@ static int selectext(char *filename)
if ((bracr=strrchr(bracl+1, ']')))
*bracr = '\0';
next = strtol(bracl+1, NULL, 0);
return next;
}
......@@ -735,9 +737,9 @@ INPUT a character string,
OUTPUT RETURN_OK if everything went fine, RETURN_ERROR otherwise.
NOTES -.
AUTHOR E. Bertin (IAP)
VERSION 14/07/2006
VERSION 23/09/2020
***/
void write_error(char *msg1, char *msg2)
void write_error(const char *msg1, const char *msg2)
{
char error[MAXCHAR];
......
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