Merge pull request #42 from astromatic/icx

Icx

INSTALL

@@ -4,7 +4,7 @@ Installing the software
 Hardware requirements
 =====================
 
-PSFEx runs in (ANSI) text-mode from a shell. A window system is
+SExtractor runs in (ANSI) text-mode from a shell. A window system is
 not necessary for basic operation.
 
 When it comes to memory usage, the amount required by SExtractor depends
@@ -75,18 +75,19 @@ locations:
    $ ./configure
 
 Compared to "gcc" and the librairies above, the combination of the
-Intel compiler ("icc") and the MKL (Math Kernel Library) libraries
-can give the SExtractor executable a significant boost in performance,
-thanks to better vectorized code, and reduced memory usage. If "icc"
-and the MKL (Math Kernel Library) are installed on your system [4],
-you can take advantage of those using instead
+Intel compiler ("icc" or "icx") and the MKL (Math Kernel Library)
+libraries can give the SExtractor executable a significant boost in
+performance, thanks to better vectorized code, and reduced memory
+usage. If "icc" (or "icx") and the MKL (Math Kernel Library) are
+installed on your system [4], you can take advantage of those using
+instead
 
    $ ./configure --enable-mkl
 
 Additionally, if the SExtractor binary is to be run on a different
-machine that does not have "icc" and the MKL (Math Kernel Library)
-installed (e.g., a cluster computing node), you must configure a
-partially statically linked executable using
+machine that does not have "icc" (or "icx") and the MKL installed
+(e.g., a cluster computing node), you must configure a partially
+statically linked executable using
 
    $ ./configure --enable-mkl --enable-auto-flags --enable-best-link
 
@@ -118,6 +119,5 @@ path).
     options "--enable-threads --enable-float".
 
 [4] The Linux versions of the Intel compiler and MKL (Math
-    Kernel Library) are available for free to academic researchers,
-    students, educators and open source contributors.
+    Kernel Library) are now available for free on Intel's website.
 

configure.ac

@@ -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:		11/03/2022
+#	Last modified:		16/09/2022
 #
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -31,8 +31,8 @@ define([AC_CACHE_LOAD],)
 define([AC_CACHE_SAVE],)
 
 # This is your standard AstrOmatic source code...
-AC_INIT(SExtractor, 2.25.3, [astromatic@astromatic.net],
-	sextractor, [http://astromatic.net/software/sextractor])
+AC_INIT([SExtractor],[2.27.0],[astromatic@astromatic.iap.fr],
+        [sextractor],[http://astromatic.net/software/sextractor])
 AC_CONFIG_MACRO_DIR([m4])
 AC_CONFIG_AUX_DIR(autoconf)
 AC_CONFIG_SRCDIR(src/makeit.c)
@@ -53,6 +53,7 @@ sinclude(acx_atlas.m4)
 sinclude(acx_openblas.m4)
 sinclude(acx_fftw.m4)
 sinclude(acx_mkl.m4)
+sinclude(acx_cfitsio.m4)
 sinclude(acx_prog_cc_optim.m4)
 sinclude(acx_pthread.m4)
 sinclude(acx_urbi_resolve_dir.m4)
@@ -79,24 +80,38 @@ AC_ARG_ENABLE(auto-flags,
 	AC_MSG_RESULT([yes]),
 	AC_MSG_RESULT([no]))
 
-# Provide special option for the Linux Intel C compiler
-AC_MSG_CHECKING([whether the INTEL compiler is enabled])
+# Provide special option for the Linux Intel C "classic" compiler
+AC_MSG_CHECKING([whether the classic INTEL compiler is enabled])
 AC_ARG_ENABLE(icc,
 	[AS_HELP_STRING([--enable-icc],
 	[Use the Intel compiler (default = no)])],
         CC="icc"
+        enable_iccx="yes"
+	AC_MSG_RESULT([yes]),
+	AC_MSG_RESULT([no]))
+
+# Provide special option for the Linux Intel OneAPI C compiler
+AC_MSG_CHECKING([whether the INTEL compiler is enabled])
+AC_ARG_ENABLE(icx,
+	[AS_HELP_STRING([--enable-icx],
+	[Use the Intel compiler (default = no)])],
+        CC="icx"
+        enable_iccx="yes"
 	AC_MSG_RESULT([yes]),
 	AC_MSG_RESULT([no]))
 
 # Provide special options for INTEL MKL
-# We force the use of icc
+# We use icc if available, if not Intel OneAPI's icx
+# (we don't use AC_PROG_CC as it does not play nice
+# in a conditional block)
 AC_MSG_CHECKING([whether INTEL's MKL is enabled])
 AC_ARG_ENABLE(mkl,
 	[AS_HELP_STRING([--enable-mkl],
 	[Use INTEL's MKL for solvers and FFTs (default = no)])],
-        enable_icc="yes"
-        CC="icc"
-	AC_MSG_RESULT([yes]),
+	    AC_MSG_RESULT([yes])
+        CC=""
+        [AC_CHECK_PROGS(CC, [icc icx cc])]
+        enable_iccx="yes",
 	AC_MSG_RESULT([no]))
 
 # Checks for programs.
@@ -115,11 +130,10 @@ AC_PROG_INSTALL
 AC_CHECK_LIB(m, sin)
 
 # Checks for header files.
-AC_HEADER_STDC
 AC_CHECK_HEADERS([fcntl.h limits.h malloc.h stdlib.h string.h sys/mman.h \
 		sys/types.h unistd.h])
 # Checks for INTEL math header files.
-if test "$enable_icc" = "yes"; then
+if test "$enable_iccx" = "yes"; then
   AC_CHECK_HEADERS(mathimf.h)
 fi
 
@@ -135,7 +149,6 @@ AC_TYPE_UID_T
 # Checks for library functions.
 AC_FUNC_ERROR_AT_LINE
 AC_FUNC_MMAP
-AC_TYPE_SIGNAL
 AC_FUNC_STAT
 AC_FUNC_STRFTIME
 AC_CHECK_FUNCS([atexit getenv gettimeofday isinf isnan logf memcpy memmove \
@@ -180,6 +193,24 @@ AC_ARG_WITH(openblas-incdir,
 	[AS_HELP_STRING([--with-openblas-incdir=<OpenBLAS header dir>],
 	[Provide an alternative path to the OpenBLAS header directory])])
 
+# Provide special option for CFITSIO
+AC_MSG_CHECKING([whether CFITSIO support should be disabled (default=enabled)])
+AC_ARG_ENABLE(cfitsio,
+	[AS_HELP_STRING([--disable-cfitsio],
+	[Disable support for compressed FITS files through the CFITSIO library (default=enabled)])],
+	if test "$enable_cfitsio" = "no"; then
+	  AC_MSG_RESULT([yes])
+	else
+	  AC_MSG_RESULT([no])
+	fi,
+	AC_MSG_RESULT([no]))
+AC_ARG_WITH(cfitsio-libdir,
+	[AS_HELP_STRING([--with-cfitsio-libdir=<CFITSIO library path>],
+	[Provide an alternative path to the CFITSIO library])])
+AC_ARG_WITH(cfitsio-incdir,
+	[AS_HELP_STRING([--with-cfitsio-incdir=<CFITSIO include dir>],
+	[Provide an alternative path to the CFITSIO include directory])])
+
 # Provide a special option for the default XSLT URL
 with_xsl_url="file://"$(URBI_RESOLVE_DIR([$datadir]))"/$PACKAGE_TARNAME/$PACKAGE_TARNAME.xsl"
 AC_ARG_WITH(xsl_url,
@@ -222,7 +253,7 @@ use_pthreads="no"
 AC_MSG_CHECKING([for profiler mode])
 AC_ARG_ENABLE(profiling,
 	[AS_HELP_STRING([--enable-profiling],
-	[Enable special mode for profiling (default = no)])]
+	[Enable special mode for profiling (default = no)])],
 	AC_MSG_RESULT([yes]),
 	AC_MSG_RESULT([no]))
 
@@ -256,10 +287,7 @@ if test "$enable_model_fitting" != "no"; then
   if test "$enable_mkl" = "yes"; then
     convlibs="${srcdir}/wcs/libwcs_c.a,${srcdir}/levmar/liblevmar.a"
     ACX_MKL($with_mkl_dir,,$enable_best_link,$convlibs)
-    if test "$MKL_WARN" == ""; then
-      AC_MSG_RESULT([yes])
-    else
-      AC_MSG_RESULT([no])
+    if test "$MKL_WARN" != ""; then
       AC_MSG_WARN([$MKL_WARN])
     fi
     AM_CFLAGS="$AM_CFLAGS $MKL_CFLAGS "
@@ -305,11 +333,21 @@ if test "$enable_model_fitting" != "no"; then
   fi
 fi
 
+########################## handle the CFITSIO library ########################
+if test "$enable_cfitsio" != "no"; then
+  ACX_CFITSIO($with_cfitsio_libdir, $with_cfitsio_incdir,
+	[LIBS="$CFITSIO_LIBS $LIBS"]
+	if test "$CFITSIO_WARN" != ""; then
+	  AC_MSG_WARN([$CFITSIO_WARN])
+	fi,
+	AC_MSG_ERROR([$CFITSIO_ERROR Exiting.]))
+fi
+
 AM_CONDITIONAL(USE_MODEL, [test "$enable_model_fitting" != "no"])
 
 # Compile with profiling option
 if test "$enable_profiling" = "yes"; then
-  if test "$enable_icc" = "yes"; then
+  if test "$enable_iccx" = "yes"; then
     AM_CFLAGS="$AM_CFLAGS -pq"
   else
     AM_CFLAGS="$AM_CFLAGS -pg"
@@ -319,9 +357,9 @@ fi
 
 # "Best" linking option
 if test "$enable_best_link" = "yes"; then
-  if test "$enable_icc" = "yes"; then
-    AM_LDFLAGS="-static-intel -qopenmp-link static -shared-libgcc \
-	-static-libtool-libs -no-intel-extensions -avoid-version $AM_LDFLAGS"
+  if test "$enable_iccx" = "yes"; then
+    AM_LDFLAGS="-static-intel -qopenmp-link=static -shared-libgcc \
+	-static-libtool-libs -avoid-version $AM_LDFLAGS"
   else
     AM_LDFLAGS="-shared-libgcc -static-libtool-libs -avoid-version $AM_LDFLAGS"
   fi

debian/rules

@@ -15,7 +15,7 @@ ifeq ($(USE_BEST),1)
 	dh_auto_configure -- --host=$(DEB_HOST_GNU_TYPE) \
 			--build=$(DEB_BUILD_GNU_TYPE) \
 			--prefix=/usr --mandir=\$${prefix}/share/man \
-			--enable-icc --enable-mkl \
+			--enable-icx --enable-mkl \
 			--enable-auto-flags --enable-best-link \
 			--with-release=$(PACKAGE_RELEASE)
 else

doc/src/conf.py

@@ -67,9 +67,9 @@ author = u'E. Bertin'
 # built documents.
 #
 # The short X.Y version.
-version = '2.25.3'
+version = '2.27.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.25.3'
+release = '2.27.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -81,7 +81,7 @@ language = None
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 #
-today = 'Fri Mar 11 2022'
+today = 'Fri Sep 16 2022'
 #
 # Else, today_fmt is used as the format for a strftime call.
 #
@@ -144,7 +144,7 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
 #
-# html_title = u'SExtractor v2.25.3'
+# html_title = u'SExtractor v2.27.0'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #

m4/acx_cfitsio.m4

+dnl
+dnl				acx_cfitsio.m4
+dnl
+dnl Figure out if the CFITSIO library and header files are installed.
+dnl
+dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+dnl
+dnl	This file part of:	AstrOmatic software
+dnl
+dnl	Copyright:		(C) 2013 Emmanuel Bertin -- IAP/CNRS/UPMC
+dnl
+dnl	License:		GNU General Public License
+dnl
+dnl	AstrOmatic software is free software: you can redistribute it and/or
+dnl	modify it under the terms of the GNU General Public License as
+dnl	published by the Free Software Foundation, either version 3 of the
+dnl	License, or (at your option) any later version.
+dnl	AstrOmatic software is distributed in the hope that it will be useful,
+dnl	but WITHOUT ANY WARRANTY; without even the implied warranty of
+dnl	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+dnl	GNU General Public License for more details.
+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:		27/02/2013
+dnl
+dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+dnl
+dnl @synopsis ACX_CFITSIO([CFITSIO_DIR, CFITSIO_INCDIR,
+dnl                    [ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]])
+dnl This macro figures out if the CFITSIO libraries and header
+dnl files are installed.
+dnl You may wish to use these variables in your default LIBS and CFLAGS:
+dnl
+dnl        LIBS="$CFITSIO_LIBS $LIBS"
+dnl
+dnl You may wish to use these variables in your default CFLAGS:
+dnl
+dnl        CFLAGS="$CFLAGS $CFITSIO_CFLAGS"
+dnl
+dnl ACTION-IF-FOUND is a list of shell commands to run if CFITSIO
+dnl is found (HAVE_CFITSIO are defined first), and ACTION-IF-NOT-FOUND
+dnl is a list of commands to run it if it is not found.
+
+AC_DEFUN([ACX_CFITSIO], [
+AC_REQUIRE([AC_CANONICAL_HOST])
+
+dnl --------------------
+dnl Search include files
+dnl --------------------
+
+acx_cfitsio_ok=no
+if test x$2 = x; then
+  AC_CHECK_HEADER(fitsio.h,[acx_cfitsio_ok=yes])
+  if test x$acx_cfitsio_ok = xyes; then
+    AC_DEFINE(CFITSIO_H, "fitsio.h", [CFITSIO header filename.])
+  else
+    AC_CHECK_HEADER(cfitsio/fitsio.h,[acx_cfitsio_ok=yes])
+    if test x$acx_cfitsio_ok = xyes; then
+      AC_DEFINE(CFITSIO_H, "cfitsio/fitsio.h", [CFITSIO header filename.])
+    else
+      CFITSIO_ERROR="CFITSIO include files not found at default location!"
+    fi
+  fi
+else
+  AC_CHECK_HEADER($2/fitsio.h,[acx_cfitsio_ok=yes])
+  if test x$acx_cfitsio_ok = xyes; then
+    AC_DEFINE_UNQUOTED(CFITSIO_H, "$2/fitsio.h", [CFITSIO header filename.])
+  else
+    CFITSIO_ERROR="CFITSIO include files not found in $2!"
+  fi
+fi
+
+dnl --------------------
+dnl Search library files
+dnl --------------------
+
+CFITSIO_LIBS=""
+OLIBS="$LIBS"
+LIBS=""
+
+if test x$acx_cfitsio_ok = xyes; then
+  if test x$1 = x; then
+    AC_CHECK_LIB(cfitsio, ffopen, [acx_cfitsio_ok=yes], [acx_cfitsio_ok=no])
+    if test x$acx_cfitsio_ok = xyes; then
+      AC_DEFINE(HAVE_CFITSIO,1, [Define if you have the CFITSIO libraries and header files.])
+      CFITSIO_LIBS="-lcfitsio"
+    else
+      CFITSIO_ERROR="CFITSIO library files not found at usual locations!"
+    fi
+  else
+dnl -------------------------
+dnl Specific libdir specified
+dnl -------------------------
+    AC_CHECK_LIB(cfitsio, ffopen, [acx_cfitsio_ok=yes], [acx_cfitsio_ok=no], [-L$1])
+    if test x$acx_cfitsio_ok = xyes; then
+      AC_DEFINE(HAVE_CFITSIO,1, [Define if you have the CFITSIO libraries and header files.])
+        CFITSIO_LIBS="-L$1 -lcfitsio"
+    else
+      CFITSIO_ERROR="CFITSIO library files not found in $1!"
+    fi
+  fi
+fi
+
+LIBS="$OLIBS"
+if test x$acx_cfitsio_ok = xyes; then
+  AC_SUBST(CFITSIO_LIBS)
+  $3
+else
+  AC_SUBST(CFITSIO_ERROR)
+  $4
+fi
+
+])dnl ACX_CFITSIO

m4/acx_mkl.m4

@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 dnl
 dnl	This file part of:	AstrOmatic software
 dnl
-dnl	Copyright:		(C) 2003-2016 IAP/CNRS/UPMC
+dnl	Copyright:		(C) 2003-2022 IAP/CNRS/SorbonneU
 dnl
 dnl	License:		GNU General Public License
 dnl
@@ -23,7 +23,7 @@ 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:		16/03/2016
+dnl	Last modified:		15/09/2022
 dnl
 dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 dnl
@@ -73,11 +73,11 @@ dnl Set architecture flags
 dnl ----------------------
 
 dnl check if INTEL compiler is present
-icc -V 2>&1 | grep -i "Intel" > /dev/null 2>&1 && flagicc=yes
+$CC -V 2>&1 | grep -i "Intel" > /dev/null 2>&1 && flagicc=yes
 dnl check if INTEL compiler uses x86_64 architecture
-icc -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 && flag64=yes
+$CC -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 && flag64=yes
 dnl check if the platform is OSX
-icc -dumpmachine 2>&1 | grep -i "darwin" > /dev/null 2>&1 && flagosx=yes
+$CC -dumpmachine 2>&1 | grep -i "darwin" > /dev/null 2>&1 && flagosx=yes
 
 dnl ----------------------
 dnl Exit if INTEL compiler is not found

m4/acx_prog_cc_optim.m4

@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 dnl
 dnl	This file part of:	AstrOmatic software
 dnl
-dnl	Copyright:		(C) 2002-2013 Emmanuel Bertin -- IAP/CNRS/UPMC
+dnl	Copyright:		(C) 2002-2022 Emmanuel Bertin -- IAP/CNRS/SorbonneU
 dnl				(C) 2002 Ville Lauriki (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:		13/03/2013
+dnl	Last modified:		07/09/2022
 dnl
 dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 dnl
@@ -60,14 +60,14 @@ EOF
       if $CC -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 &&
            $CC -c -O conftest.c > /dev/null 2>&1 &&
            test -f conftest.o; then
-        prog_cc_optim_cv_flags="-O3 -axSSSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I -no-prec-div -unroll"
+        prog_cc_optim_cv_flags="-O3 -axSSSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I"
         prog_ld_optim_cv_flags=""
 
       dnl INTEL C 32bits compiler
       elif $CC -V 2>&1 | grep -i "Intel(R)" > /dev/null 2>&1 &&
            $CC -c -O conftest.c > /dev/null 2>&1 &&
            test -f conftest.o; then
-        prog_cc_optim_cv_flags="-O3 -axSSE2,SSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I -no-prec-div -unroll"
+        prog_cc_optim_cv_flags="-O3 -axSSE2,SSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I"
         prog_ld_optim_cv_flags=""
 
       dnl GCC

m4/acx_pthread.m4

@@ -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

@@ -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

@@ -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

@@ -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)");

src/catout.c

@@ -1059,7 +1059,7 @@ void	reendcat()
   {
    keystruct	*key;
    tabstruct	*tab;
-   OFF_T	pos;
+   OFF_T2	pos;
    char		*head;
 
   switch(prefs.cat_type)
@@ -1127,4 +1127,3 @@ void	zerocat(void)
   }
 
 
-

src/define.h

@@ -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

@@ -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

@@ -7,7 +7,7 @@
 *
 *	This file part of:	SExtractor
 *
-*	Copyright:		(C) 1993-2012 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:		12/07/2012
+*	Last modified:		23/09/2020
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -70,6 +70,10 @@ picstruct	*newfield(char *filename, int flags, int ext)
   field->cat = cat;
   nok = 0;
   tab = cat->tab;
+#ifdef HAVE_CFITSIO
+  if (tab->isTileCompressed)
+    nok++;
+#endif
   if (tab->naxis >= 2
 	&& strncmp(tab->xtension, "BINTABLE", 8)
 	&& strncmp(tab->xtension, "ASCTABLE", 8))
@@ -78,6 +82,10 @@ picstruct	*newfield(char *filename, int flags, int ext)
   for (ntab=cat->ntab; ext2-- && ntab--;)
     {
     tab=tab->nexttab;
+#ifdef HAVE_CFITSIO
+    if (tab->isTileCompressed)
+      nok++;
+#endif
     if (tab->naxis >= 2
 	&& strncmp(tab->xtension, "BINTABLE", 8)
 	&& strncmp(tab->xtension, "ASCTABLE", 8))

src/fits/fitsbody.c

@@ -7,7 +7,7 @@
 *
 *	This file part of:	AstrOmatic FITS/LDAC library
 *
-*	Copyright:		(C) 1995-2010 IAP/CNRS/SorbonneU
+*	Copyright:		(C) 1995-2020 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:		26/08/2020
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -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)
@@ -304,7 +395,7 @@ INPUT	A pointer to the tab structure,
 OUTPUT	-.
 NOTES	.
 AUTHOR	E. Bertin (IAP)
-VERSION	11/02/2020
+VERSION	26/08/2020
  ***/
 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)
+       	  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

@@ -23,7 +23,7 @@
 *	along with AstrOmatic software.
 *	If not, see <http://www.gnu.org/licenses/>.
 *
-*	Last modified:		15/07/2020
+*	Last modified:		26/08/2020
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -167,6 +167,33 @@ int	close_cat(catstruct *cat)
   return RETURN_OK;
   }
 
+#ifdef	HAVE_CFITSIO
+/****** close_cfitsio **************************************************************
+
+Closes a file previously opened by cfitsio 
+
+***/
+int	close_cfitsio(fitsfile *infptr)
+{
+
+	if (infptr != NULL) {
+
+		int status = 0; fits_close_file(infptr, &status);
+		if (status != 0) {
+			fits_report_error(stderr, status);
+			printf("ERROR could not close FITS file with cfitsio\n");
+		}
+		else {
+			//printf("Successfully closed FITS file with cfitsio\n");
+			infptr == NULL;
+		}
+	}
+	else {
+	    //printf("ERROR no cfitsio file to close\n");
+	}
+}
+#endif // HAVE_CFITSIO
+
 
 /****** free_cat ***************************************************************
 PROTO	void free_cat(catstruct **cat, int ncat)
@@ -325,14 +352,55 @@ 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;
+   status = 0; fits_open_file(&infptr, cat->filename, READONLY, &status);
+   if (status != 0) {
+     fits_report_error(stderr, status);
+     printf("ERROR could not open FITS file with cfitsio: %s\n", cat->filename);
+   }
+   hdunum = 1;
+
+  int any_tile_compressed = 0;
+#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) {
+
+      any_tile_compressed = 1;
+      tab->hdunum = hdunum;
+      tab->infptr = infptr;
+
+      status = 0; fits_movabs_hdu(tab->infptr, tab->hdunum, &hdutype, &status);
+      if (status != 0) printf("ERROR could not move to hdu %d in file %s\n", tab->hdunum, cat->filename);
+
+      if (tab->tabsize)
+        fseek(cat->file, infptr->Fptr->headstart[hdunum], SEEK_SET);
+    }
+    // NOT tile-compressed
+    else {
+
+      tab->infptr = NULL;
+
+      if (tab->tabsize)
+        QFSEEK(cat->file, PADTOTAL(tab->tabsize), SEEK_CUR, cat->filename);
+    }
+
+    hdunum++;
+#else
     if (tab->tabsize)
       QFSEEK(cat->file, PADTOTAL(tab->tabsize), SEEK_CUR, cat->filename);
+#endif // HAVE_CFITSIO
+
     if (prevtab)
       {
       tab->prevtab = prevtab;
@@ -346,6 +414,12 @@ int	map_cat(catstruct *cat)
     QFTELL(cat->file, tab->headpos, cat->filename);
     }
 
+#ifdef	HAVE_CFITSIO
+  // we will not need CFitsIO, so close CFitsIO file pointer now
+  if (!any_tile_compressed)
+    close_cfitsio(infptr);
+#endif
+
   cat->ntab = ntab;
   free(tab);
   if (prevtab)

src/fits/fitscat.h

@@ -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
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -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 ---------------------------------*/
@@ -180,8 +185,8 @@ 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 */
@@ -191,6 +196,12 @@ typedef struct structtab
   int		swapflag;		/* mapped to a swap file ? */
   char		swapname[MAXCHARS];	/* name of the swapfile */
   unsigned int	bodysum;		/* Checksum of the FITS body */
+#ifdef HAVE_CFITSIO
+  fitsfile *infptr;                     /* a cfitsio pointer to the file */
+  int hdunum;                           /* FITS HDU number for this 'table' */
+  int isTileCompressed;                 /* is this a tile compressed image?  */
+  long currentElement;                  /* tracks the current image pixel */
+#endif
   }		tabstruct;
 
 
@@ -218,8 +229,8 @@ 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 +282,9 @@ 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(fitsfile *infptr),
+#endif
 		copy_key(tabstruct *tabin, char *keyname, tabstruct *tabout,
 			int pos),
 		copy_tab(catstruct *catin, char *tabname, int seg,
@@ -328,8 +342,4 @@ 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

@@ -101,29 +101,38 @@ INPUT	pointer to catstruct.
 OUTPUT	-.
 NOTES	-.
 AUTHOR	E. Bertin (IAP)
-VERSION	03/06/2012
+VERSION	04/12/2019
  ***/
 void	readbasic_head(tabstruct *tab)
 
   {
    char		str[88];
-   char		key[12], name[16],
+   char		key[12], name[16], bitpix_key[16], naxis_key[16],
 		*filename;
    int		i;
    KINGSIZE_T	tabsize;
 
   filename = (tab->cat? tab->cat->filename : strcpy(name, "internal header"));
-
-  if (fitsread(tab->headbuf, "BITPIX  ", &tab->bitpix, H_INT, T_LONG)
+  strncpy(bitpix_key, "BITPIX  ", 9);
+  strncpy(naxis_key, "NAXIS   ", 9);
+
+#ifdef HAVE_CFITSIO
+  tab->isTileCompressed = (fitsread(tab->headbuf, "ZIMAGE  ",
+			str, H_STRING, T_STRING) == RETURN_OK)? 1 : 0;
+  if (tab->isTileCompressed) {
+    strncpy(bitpix_key, "ZBITPIX ", 9);
+    strncpy(naxis_key, "ZNAXIS  ", 9);
+  }
+#endif
+  if (fitsread(tab->headbuf, bitpix_key, &tab->bitpix, H_INT, T_LONG)
 	==RETURN_ERROR)
     error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
 
-  tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
-
-  if (fitsread(tab->headbuf, "NAXIS   ", &tab->naxis, H_INT, T_LONG)
+  if (fitsread(tab->headbuf, naxis_key, &tab->naxis, H_INT, T_LONG)
 	==RETURN_ERROR)
     error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
 
+  tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
   tabsize = 0;
   if (tab->naxis>0)
     {
@@ -133,6 +142,11 @@ void	readbasic_head(tabstruct *tab)
     tabsize = 1;
     for (i=0; i<tab->naxis && i<999; i++)
       {
+#ifdef HAVE_CFITSIO
+       if (tab->isTileCompressed)
+         sprintf(key,"ZNAXIS%-2d", i+1);
+       else
+#endif
       sprintf(key,"NAXIS%-3d", i+1);
       if (fitsread(tab->headbuf, key, &tab->naxisn[i], H_INT, T_LONG)
 		==RETURN_ERROR)
@@ -144,6 +158,13 @@ void	readbasic_head(tabstruct *tab)
 /*random groups parameters (optional)*/
   tab->pcount = 0;
   fitsread(tab->headbuf, "PCOUNT  ", &tab->pcount, H_INT, T_LONG);
+
+#ifdef HAVE_CFITSIO
+  // CFITSIO TODO HACK
+  if (tab->isTileCompressed)
+    tab->pcount = 0;
+#endif
+
   tab->gcount = 1;
   fitsread(tab->headbuf, "GCOUNT  ", &tab->gcount, H_INT, T_LONG);
 
@@ -284,7 +305,12 @@ 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*/

src/fits/fitskey.c

@@ -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;
   }