Commit 58245677 authored by Emmanuel Bertin's avatar Emmanuel Bertin
Browse files

Merge branch 'cfitsio' into icx

parents 9689a1c4 37680dba

configure.ac

+30 −1
Original line number Diff line number Diff line
@@ -31,7 +31,7 @@ define([AC_CACHE_LOAD],) 
define([AC_CACHE_SAVE],)



# This is your standard AstrOmatic source code...

AC_INIT(SExtractor, 2.25.3, [astromatic@astromatic.net],

AC_INIT(SExtractor, 2.27.0, [astromatic@astromatic.net],

	sextractor, [http://astromatic.net/software/sextractor])

AC_CONFIG_MACRO_DIR([m4])

AC_CONFIG_AUX_DIR(autoconf)
@@ -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)
@@ -180,6 +181,24 @@ 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,
@@ -305,6 +324,16 @@ 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

doc/src/conf.py

+10 −2
Original line number Diff line number Diff line
@@ -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 +81,11 @@ language = None 
# There are two options for replacing |today|: either, you set today to some

# non-false value, then it is used:

#

<<<<<<< HEAD

today = 'Fri Mar 11 2022'

=======

today = 'Tue Sep 06 2022'

>>>>>>> cfitsio

#

# Else, today_fmt is used as the format for a strftime call.

#
@@ -144,7 +148,11 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] 
# The name for this set of Sphinx documents.

# "<project> v<release> documentation" by default.

#

<<<<<<< HEAD

# html_title = u'SExtractor v2.25.3'

=======

# html_title = u'SExtractor v2.27.0'

>>>>>>> cfitsio



# A shorter title for the navigation bar.  Default is the same as html_title.

#

m4/acx_cfitsio.m4

0 → 100644
+115 −0
Original line number Diff line number Diff line 
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

src/analyse.c

+3 −4
Original line number Diff line number Diff line
@@ -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)

      {

src/back.c

+66 −18
Original line number Diff line number Diff line
@@ -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)");