Moved codebase to new autogen.sh pre-configure stage.

ASSOC options do not work properly with MEF images (this is not really a bug).

				Emmanuel Bertin <bertin@iap.fr>

Copyright 2010 IAP - CNRS / Universite P.&M.Curie

Copyright 2010 - 2017 IAP / CNRS / Universite P.&M.Curie

Author:	  Emmanuel Bertin <bertin@iap.fr>

Main author:	  Emmanuel Bertin <bertin@iap.fr>

SExtractor is free software: you can redistribute it and/or

modify it under the terms of the GNU General Public License as

#

#	This file part of:	SExtractor

#

#	Copyright:		(C) 1997-2010 Emmanuel Bertin -- IAP/CNRS/UPMC

#	Copyright:		(C) 1997-2017 IAP/CNRS/UPMC

#

#	License:		GNU General Public License

#

#	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:		11/10/2010

#	Last modified:		19/06/2017

#

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

------------------------------------------------------------------------

r381 | bertin | 2016-03-08 22:35:51 +0100 (Tue, 08 Mar 2016) | 2 lines

Added missing dgeo.c and dgeo.h files.

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r380 | bertin | 2016-03-08 18:02:20 +0100 (Tue, 08 Mar 2016) | 13 lines

Fixed PCi_j WCS keyword parsing issue (thanks to O.Fors for reporting this issue).

Fixed issue with magnitudes when used as PSF model parameters (thanks to A.Donnarumma for reporting this issue).

Added ID_PARENT catalog parameter to identify the common parent of deblended sources (thanks to R.McMahon for the suggestion).

Introduced regularization of Sersic model ellipticities based on AMALGAm prescriptions for the Great3 challenge (see Mandelbaum et al. 2015).

Fixed error in ecliptic coordinate computations (thanks to H.Bouy for reporting this issue).

Added support for differential geometry maps, with new DGEO_TYPE and DGEO_IMAGE configuration keywords and new DGEOX/Y_IMAGE and DGEOX/YWIN_IMAGE measurement parameters.

Added differential geometry map correction to model-fitting.

Added VIGNET_DGEOX and VIGNET_DGEOY differential geometry map cutouts in catalogs (for use in PSFEx).

Added support for PSF model dependencies in ASSOC vectors.

Fixed issue with single-line background meshes.

Fixed positional offsets of large galaxy models on MODELS and -MODELS check-images.

Pushed version number to 2.23.1.

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r332 | bertin | 2014-03-19 14:56:33 +0100 (Wed, 19 Mar 2014) | 3 lines

Refactored management of aspect ratios in model-fitting.

Pushed version number to 2.19.5.

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r323 | bertin | 2013-09-24 10:03:28 +0200 (Tue, 24 Sep 2013) | 4 lines

Fixed positional offsets of large galaxy models on MODELS and -MODELS check-ima\

ges.

Pushed version number to 2.19.4.

------------------------------------------------------------------------

r321 | bertin | 2013-09-12 14:44:12 +0200 (Thu, 12 Sep 2013) | 2 lines

Added missing reset of measurements parameters at each catalog initialization.

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r320 | bertin | 2013-09-12 14:09:40 +0200 (Thu, 12 Sep 2013) | 5 lines

Fixed regression with --disable-model-fitting option.

Fixed issue with model fitting measurement leftovers with masked sources (thank

s to E. Rykoff).

Pushed version number to 2.19.3.

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r319 | marmo | 2013-08-17 22:41:03 +0200 (Sat, 17 Aug 2013) | 2 lines

Solved issue with --disable-model-fitting configuration option. Pushed version number to 2.19.2

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r314 | bertin | 2013-07-17 17:00:34 +0200 (Wed, 17 Jul 2013) | 2 lines

Fixed obsolete SExtractor measurement parameters in "make check" tests.

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r313 | bertin | 2013-07-17 16:40:17 +0200 (Wed, 17 Jul 2013) | 3 lines

Fixed compilation issue with finitef() function in profit.c on OSX 10.8.

Pushed version number to 2.19.1.

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r312 | bertin | 2013-07-05 15:52:54 +0200 (Fri, 05 Jul 2013) | 10 lines

Fixed issue with MINIBACKGROUND	and MINIBACK_RMS multi-extension check-images.

Added new measurement parameters:

FLUXRATIO_POINTSOURCE :    Point-source flux-to-total ratio from fitting,

FLUXRATIOERR_POINTSOURCE : Uncertainty on point-source flux-to-total ratio,

FLUXRATIO_SPHEROID :       Spheroid flux-to-total ratio from fitting,

FLUXRATIOERR_SPHEROID :    Uncertainty on spheroid flux-to-total ratio,

FLUXRATIO_DISK :           Disk flux-to-total ratio from fitting, and

FLUXRATIOERR_DISK :        Uncertainty on disk flux-to-total ratio.

Pushed version number to 2.19.0

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r311 | bertin | 2013-06-18 12:35:54 +0200 (Tue, 18 Jun 2013) | 2 lines

Fixed uninitialized 2nd BACK_VALUE in double image + BACK_TYPE MANUAL modes.

------------------------------------------------------------------------

r310 | bertin | 2013-06-06 17:06:51 +0200 (Thu, 06 Jun 2013) | 3 lines

Fixed missing image name in sex.xml VOTable output in double image mode when input filenames are separated by a comma instead of a space.

Pushed version number to 2.18.12

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r309 | bertin | 2013-04-27 15:35:48 +0200 (Sat, 27 Apr 2013) | 8 lines

Fixed issue with ASSOC_TYPE NEAREST (Thanks to V. de Lapparent).

Fixed regression with Eli Rykoff's fixes.

Fixed issue with FFTW includes.

Fixed typos in VOTable output.

Added translation of Boolean T and F to Y and N in XSLT.

Added --with-mkl-dir option in configure.

Pushed version number to 2.18.11.

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r307 | bertin | 2013-04-05 10:23:35 +0200 (Fri, 05 Apr 2013) | 3 lines

Added proper correction of model subsampling to SPHEROIDS and DISKS check-images.

Pushed version number to 2.18.9.

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r306 | bertin | 2013-04-04 17:54:11 +0200 (Thu, 04 Apr 2013) | 2 lines

Fixed typo in acx_mkl (no consequence here).

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r305 | bertin | 2013-04-04 00:04:38 +0200 (Thu, 04 Apr 2013) | 11 lines

Added support for Gaussian priors on (transformed) model parameters (deactivated).

Fixed model sub-sampling issues with large objects, including check-image resizing.

Fixed initialization of DETMODEL size guess (thanks to Eli Rykoff).

Fixed image extension pb in double weighting/single image mode.

Improved debug info for memory allocations in FFT and FITS libraries.

Fixed crashes with DETMODEL magnitudes on null measurement weight maps.

Added Eli Rykoff's fix to discard sources with NaNs in the fitted positions.

Improved MKL autoconfiguration.

Improved vectorization in FITS data transformations and FFT-based convolutions.

Pushed SExtractor version number to 3.18.8.

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r302 | bertin | 2012-09-23 18:27:09 +0200 (Sun, 23 Sep 2012) | 4 lines

Fixed issue with the position, positional uncertainties and flux of (large) sub-sampled models.

Fixed padding issue for binary FITS catalogs >2GB.

Pushed version number to 2.18.4.

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r300 | bertin | 2012-07-19 18:21:32 +0200 (Thu, 19 Jul 2012) | 4 lines

Added support for CORE-AVX2 and CORE-AVC-I optimized code when using INTEL compiler.

Added better control of the number of threads used in MKL library calls (when used).

Pushed version number to 2.18.3.

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r298 | bertin | 2012-07-17 22:20:15 +0200 (Tue, 17 Jul 2012) | 3 lines

Fixed issue with --with-fftw-libdir configure option (thanks to John P. Marriner).

Fixed minor issue with the reading of TNX and TPV WCS coefficients.

------------------------------------------------------------------------

r297 | bertin | 2012-07-12 18:05:39 +0200 (Thu, 12 Jul 2012) | 5 lines

Fixed regression with FITS image extension numbering.

Fixed issues with PSF image extension numbering.

Fixed crashes when calling FFT routines with the MKL library.

Pushed version number to 2.18.2.

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r296 | bertin | 2012-07-12 11:31:00 +0200 (Thu, 12 Jul 2012) | 3 lines

Replaced --enable-gprof configuration with --enable-profiling.

Switched on --enable-mkl for make rpm-best.

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r295 | bertin | 2012-07-11 18:51:29 +0200 (Wed, 11 Jul 2012) | 5 lines

Fixed obsolete autoconf macros in configure.ac

Added control of the number of threads in MKL calls.

Added support for negative NTHREADS (= max number of threads).

Pushed version number to 2.18.1.

------------------------------------------------------------------------

r294 | bertin | 2012-07-10 00:02:36 +0200 (Tue, 10 Jul 2012) | 4 lines

Added support for the INTEL MKL library in place of ATLAS and FFTW (configure --enable-mkl option).

Updated LevMar library to V2.6.

Pushed version number to 2.18.0.

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r293 | bertin | 2012-07-09 10:53:30 +0200 (Mon, 09 Jul 2012) | 5 lines

Updated WCS library: fixed issue with TPV CTYPEs and added support for MJDSTART header keyword.

Updated FITS library to the latest version, removing potential conflicts with the CFITSIO library.

Added PSF/model-fitting support for MEFs.

Pushed version number to 2.17.0

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r292 | bertin | 2012-06-06 22:01:59 +0200 (Wed, 06 Jun 2012) | 2 lines

Fixed Inf in some instances of SPREADERR_MODEL.

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r291 | bertin | 2012-06-03 21:43:35 +0200 (Sun, 03 Jun 2012) | 3 lines

Fixed obsolete behaviour with 8 bit images (would suppose 8 bit integers  are signed by default).

Pushed version number to 2.16.3.

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r290 | bertin | 2012-06-01 21:08:09 +0200 (Fri, 01 Jun 2012) | 4 lines

Fixed sporadic occurences of NaN in SPREADERR_MODEL and ERRBMODEL_IMAGE.

Updated WCS library to the latest version.

Pushed version number to 2.16.2.

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r284 | bertin | 2012-04-18 13:57:02 +0200 (Wed, 18 Apr 2012) | 12 lines

Fixed potential issues in ASSOCCOORD_TYPE WORLD mode.

Fixed triggering of model surface brightness measurement.

Added new FLUX_DETMODEL,FLUXERR_DETMODEL, MAG_DETMODEL,MAGERR_DETMODEL, FLAGS_DE

TMODEL and CHI2_DETMODEL measurement parameters that apply on the measurement im

age a model fitted on the detection image (two PSF models required); these new p

arameters are meant for measuring faint galaxy colors.

Improved displayed info for memory allocation failures.

Increased default maximum number of threads set by configure to 1024.

Updated Copyright display line (2012).

Added support for "TPV" WCS projection.

Pushed version number to 2.16.0.

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r271 | bertin | 2011-10-08 22:31:03 +0200 (Sat, 08 Oct 2011) | 2 lines

Fixed large memory leak in model-fitting.

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r265 | bertin | 2011-09-06 19:08:22 +0200 (Tue, 06 Sep 2011) | 2 lines

Fixed triggering of model surface brightness measurement.

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r264 | bertin | 2011-09-06 17:46:57 +0200 (Tue, 06 Sep 2011) | 5 lines

Fixed scaling issue with surface brightness measurements on galaxy models (thanks to V. de Lapparent).

Optimized the setup of astrometric polynoms.

Removed confusing FITS header keywords from non-MEF check-images.

Pushed version number to 2.14.7.

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r263 | bertin | 2011-08-22 15:11:43 +0200 (Mon, 22 Aug 2011) | 3 lines

Removed (dummy) WCS information from FITS_1.0 catalog primary header (thanks to H.J. McCracken for reporting).

Pushed version number to 2.14.5

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r262 | bertin | 2011-08-05 16:14:18 +0200 (Fri, 05 Aug 2011) | 2 lines

Added missing README in src/wcs/ subdirectory.

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r261 | bertin | 2011-08-05 16:13:20 +0200 (Fri, 05 Aug 2011) | 2 lines

Added forgotten LICENSE file in main directory.

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r257 | bertin | 2011-07-25 11:49:12 +0200 (Mon, 25 Jul 2011) | 2 lines

Replaced a third missing F in HAVE_SINCOSF!

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r256 | bertin | 2011-07-25 10:43:22 +0200 (Mon, 25 Jul 2011) | 2 lines

Replaced a second missing F in HAVE_SINCOSF.

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r255 | bertin | 2011-07-25 10:23:25 +0200 (Mon, 25 Jul 2011) | 2 lines

Had forgotten the final F in HAVE_SINCOSF in add_prof().

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r254 | bertin | 2011-07-25 10:20:17 +0200 (Mon, 25 Jul 2011) | 5 lines

Fixed missing test for sincosf() that prevented the code to compile on MacOS (thanks to C.Aspin).

Added support for RADESYS WCS keyword (non-standard RADECSYS still supported).

Fixed display precision issues with SPREAD_MODEL.

Pushed version number to 2.14.4.

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r250 | bertin | 2011-07-01 15:49:04 +0200 (Fri, 01 Jul 2011) | 4 lines

Fixed issue with FWHMPSF_WORLD.

Added support for AVX extensions with INTEL compiler v12.

Version number pushed to 2.14.2.

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r246 | bertin | 2011-05-31 22:07:38 +0200 (Tue, 31 May 2011) | 4 lines

Fixed regression involving SPREAD_MODEL and SPREADERR_MODEL (Thanks Shantanu for reporting).

Added Rescale_Weights PARAM in XML output.

Pushed version number to 2.14.1

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r244 | bertin | 2011-05-06 15:45:20 +0200 (Fri, 06 May 2011) | 8 lines

Fixed FLUX_HYBRID and MAG_HYBRID centering issues.

Added 2nd order moments measurements of the convolved model.

Fixed issues introduced in a recent updates with check-images.

Implemented new algorithms for SPREAD_MODEL and SPREADERR_MODEL (no optimization yet and the scaling is still variable however).

Added experimental SNR_WIN measurement parameter.

Fixed crash with empty ASSOC lists.

Pushed version number to 2.13.6.

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r243 | bertin | 2011-03-13 17:52:46 +0100 (Sun, 13 Mar 2011) | 3 lines

Added one extra decimal to position measurements in pixel coordinates.

Preliminary implementation of a RESCALE_WEIGHTS configuration switch.

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r242 | bertin | 2011-01-26 11:34:58 +0100 (Wed, 26 Jan 2011) | 2 lines

Added missing .vcproj distribution files in LevMar library directory.

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r241 | bertin | 2011-01-25 01:16:47 +0100 (Tue, 25 Jan 2011) | 4 lines

Added new ASSOCCOORD_TYPE configuration parameter for ASSOCiating detections either in PIXEL or WORLD coordinates.

Fixed sampling issues for Sersic, de Vaucouleurs and exponential model-fitting.

Version number pushed to 2.13.2.

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r239 | bertin | 2010-12-02 18:58:35 +0100 (Thu, 02 Dec 2010) | 2 lines

Fixed issue with output Check-image headers when reading individual extensions from MEFs (thanks to user Lantern for the bug report).

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r236 | bertin | 2010-11-11 15:55:08 +0100 (Thu, 11 Nov 2010) | 4 lines

Fixed issue with zero-sized columns in FITS binary tables,

Removed unused variables in poly.c.

Fixed issue with invalid comment in XSL stylesheet.

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r235 | bertin | 2010-10-25 22:50:17 +0200 (Mon, 25 Oct 2010) | 2 lines

Added FLUXHYBRID_,MAG_HYBRID

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r234 | bertin | 2010-10-14 16:06:58 +0200 (Thu, 14 Oct 2010) | 3 lines

Fixed issue with duplicated sources when PSF_NMAX is >1.

Pushed version number to 2.13.1.

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r233 | bertin | 2010-10-11 18:14:04 +0200 (Mon, 11 Oct 2010) | 11 lines

Moved the whole package back to GPL.

Added more complete headers to all files.

Clarified licensing issues.

Updated FITS library.

Updated configuration files.

Added configuration files to the list of data that get installed in ${prefix}/share/sextractor.

Added background offset and point-source model components: FLUX_BACKOFFSET,FLUXERR_BACKOFFSET,FLUX_POINTSOURCE,FLUXERR_POINTSOURCE,MAG_POINTSOURCE,MAGERR_POINTSOURCE.

Tweaked model-fitting convergence parameters.

Fixed catalogue source ordering/number issue in dual-image mode.

Pushed version number to 2.13.0.

------------------------------------------------------------------------

r231 | bertin | 2010-09-29 17:11:15 +0200 (Wed, 29 Sep 2010) | 3 lines

June 2017: 2.24

	- Auto-config based on autogen.sh

	- Main repository moved to GitHub

October 2010: 2.13

	- Adaptive CLASS_STAR

	- Model-fitting.

Copyright 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software

Foundation, Inc.

Installing the software

***********************

Hardware requirements

=====================

PSFEx 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

mostly on the size of the input images and especially on the presence of

the so-called "check images". But in most cases it is less than one

gigabyte.

   This file is free documentation; the Free Software Foundation gives

unlimited permission to copy, distribute and modify it.

Basic Installation

==================

The simplest way to compile this package is:

Obtaining SExtractor

====================

  1. `cd' to the directory containing the package's source code and type

     `./configure' to configure the package for your system.

  2. Type `make' to compile the package.

  3. Type `make install' to install the programs and any data files and

     documentation.

For Linux users, the simplest way to have SExtractor up and running is

to install the standard binary package that comes with your Linux

distribution. Run, e.g., "apt-get sextractor" (on Debian) or

"dnf install sextractor" (Fedora) and SExtractor, as well as all its

dependencies, will automatically be installed. If you decided to install

the package this way you're all set!

However if SExtractor is not available in your distribution, or to

obtain the most recent version, the SExtractor source package can be

downloaded from the official GitHub repository. One may choose one of

the stable releases, or for the fearless, a copy of the current master

development branch.

Compilers and Options

Software requirements

=====================

   Some systems require unusual options for compilation or linking that

the `configure' script does not know about.  Run `./configure --help'

for details on some of the pertinent environment variables.

SExtractor has been developed on GNU/Linux machines and should compile

on any POSIX-compliant system (this includes Apple OS X and Cygwin

on Microsoft Windows, at the price of some difficulties with the

configuration), provided that the development packages of the

following libraries have been installed:

* ATLAS V3.6 and above [2],

* FFTw V3.0 and above [3],

On Fedora/Redhat distributions for instance, the development packages

above are available as "atlas-devel" and "fftw-devel".

ATLAS and FFTw are not necessary if SExtractor is linked with

Intel's MKL (Math Kernel Library) library.

Installation

============

To install from the GitHub source package, you must first uncompress

the archive:

   $ unzip sextractor-<version>.zip

A new directory called "sextractor-<version>" should now appear at the

current location on your disk. Enter the directory and generate the

files required by the autotools, which the package relies on:

   $ cd sextractor-<version>

   $ sh autogen.sh

A "configure" script is created. This script has many options, which

may be listed with the "--help" option:

   $ ./configure --help

No options are required for compiling with the default GNU C compiler

("gcc") if all the required libraries are installed at their default

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

   $ ./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

   $ ./configure --enable-mkl --enable-auto-flags --enable-best-link

In all cases, SExtractor can now be compiled with

   $ make -j

An "src/sex" executable is created. For system-wide installation,

run the usual

   $ sudo make install

   You can give `configure' initial values for variables by setting

them in the environment.  You can do that on the command line like this:

You may now check that the software is properly installed by simply

typing in your shell:

     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix

   $ sex

(note that some shells require the "rehash" command to be run before

making a freshly installed executable accessible in the execution

path).

Installation Names

==================

[1] Mac OS X ".dmg" packages should be available soon.

   By default, `make install' will install the package's files in

`/usr/local/bin', `/usr/local/man', etc.  You can specify an

installation prefix other than `/usr/local' by giving `configure' the

option `--prefix=PATH'.

[2] Use the "--with-atlas" and/or "--with-atlas-incdir" options of

    the SExtractor "configure" script to specify the ATLAS library and

    include paths if ATLAS files are installed at unusual locations.

   You can specify separate installation prefixes for

architecture-specific files and architecture-independent files.  If you

give `configure' the option `--exec-prefix=PATH', the package will use

PATH as the prefix for installing programs and libraries.

Documentation and other data files will still use the regular prefix.

[3] Make sure that FFTw has been compiled with "configure"

    options "--enable-threads --enable-float".

   In addition, if you use an unusual directory layout you can give

options like `--bindir=PATH' to specify different values for particular

kinds of files.  Run `configure --help' for a list of the directories

you can set and what kinds of files go in them.

[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.