Merge branch 'Pearsons' into doc

#

#	This file part of:	SExtractor

#

#	Copyright:		(C) 2002-2023 IAP/CNRS/SorbonneU

#	Copyright:		(C) 2002-2023 CFHT/IAP/CNRS/SorbonneU

#

#	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:		26/02/2023

#	Last modified:		07/03/2023

#

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

define([AC_CACHE_SAVE],)

# This is your standard AstrOmatic source code...

AC_INIT([SExtractor],[2.27.1],[astromatic@astromatic.iap.fr],

AC_INIT([SExtractor],[2.28.0],[astromatic@astromatic.iap.fr],

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

AC_CONFIG_MACRO_DIR([m4])

AC_CONFIG_AUX_DIR(autoconf)

# add these directories to sys.path here. If the directory is relative to the

# documentation root, use os.path.abspath to make it absolute, like shown here.

#

import os, sys

sys.path.insert(0, os.path.abspath('.'))

# import os

# import sys

# sys.path.insert(0, os.path.abspath('.'))

import sphinx_rtd_theme

import adsarxiv

# -- General configuration ---------------------------------------------------

# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.

#

# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be

# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom

# ones.

extensions = [

    'sphinxcontrib.bibtex',

    'sphinx.ext.githubpages',

#   'sphinx.ext.intersphinx',

#   'sphinx.ext.todo',

    'sphinx.ext.mathjax',

    'sphinx.ext.todo',

    'sphinxcontrib.bibtex',

    'sphinx.ext.githubpages'

]

# Add any paths that contain templates here, relative to this directory.

templates_path = ['../theme']

templates_path = ['_templates']

# The suffix(es) of source filenames.

# You can specify multiple suffix as a list of string:

# General information about the project.

project = u'SExtractor'

filename = 'sextractor'

copyright = u'2017-2023, CFHT/IAP/CNRS/SorbonneU'

copyright = u'2017, IAP/CNRS/UPMC'

author = u'E. Bertin'

# The version info for the project you're documenting, acts as replacement for

# built documents.

#

# The short X.Y version.

version = '2.27.1'

version = '2.28.0'

# The full version, including alpha/beta/rc tags.

release = '2.27.1'

release = '2.28.0'

# The language for content autogenerated by Sphinx. Refer to documentation

# for a list of supported languages.

#

# This is also used if you do content translation via gettext catalogs.

# Usually you set "language" from the command line for these cases.

language = None

# There are two options for replacing |today|: either, you set today to some

# non-false value, then it is used:

# List of patterns, relative to source directory, that match files and

# directories to ignore when looking for source files.

# This patterns also effect to html_static_path and html_extra_path

exclude_patterns = ['global.rst','keys.rst','macro.rst','roles.rst']

exclude_patterns = ['global.rst','keys.rst','roles.rst']

# The reST default role (used for this markup: `text`) to use for all

# documents.

#

# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.

#

# add_function_parentheses = True

# If true, the current module name will be prepended to all description

# unit titles (such as .. function::).

#

# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the

# output. They are ignored by default.

# The name of the Pygments (syntax highlighting) style to use.

pygments_style = 'sphinx'

numfig = True

# A list of ignored prefixes for module index sorting.

# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built documents.

# keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.

todo_include_todos = True

smartquotes = False

numfig = True

# -- Options for HTML output -------------------------------------------------

# -- Options for HTML output ----------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for

# a list of builtin themes.

#

html_theme = 'sphinx_rtd_theme'

# Theme options are theme-specific and customize the look and feel of a theme

# further.  For a list of options available for each theme, see the

# documentation.

#

# html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.

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 v2.28.0'

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

#

# html_short_title = None

# The name of an image file (relative to this directory) to place at the top

# of the sidebar.

#

# html_logo = None

# The name of an image file (relative to this directory) to use as a favicon of

# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32

# pixels large.

#

# html_favicon = None

# Add any paths that contain custom static files (such as style sheets) here,

# relative to this directory. They are copied after the builtin static files,

# so a file named "default.css" will overwrite the builtin "default.css".

# Trick for having ReadTheDocs read custom theme changes

def setup(app):

    app.add_css_file("css/custom.css")

    app.add_stylesheet("css/custom.css")

# Add any extra paths that contain custom files (such as robots.txt or

# .htaccess) here, relative to this directory. These files are copied

# directly to the root of the documentation.

#

# html_extra_path = []

# If not None, a 'Last updated on:' timestamp is inserted at every page

# bottom, using the given strftime format.

# The empty string is equivalent to '%b %d, %Y'.

#

# html_last_updated_fmt = None

# If true, SmartyPants will be used to convert quotes and dashes to

# typographically correct entities.

#

# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.

#

# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names to

# template names.

#

# html_additional_pages = {}

# If false, no module index is generated.

#

# html_domain_indices = True

# If false, no index is generated.

#

# html_use_index = True

# If true, the index is split into individual pages for each letter.

#

# html_split_index = False

# If true, links to the reST sources are added to the pages.

#

html_show_sourcelink = False

# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.

#

# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.

#

html_show_copyright = True

# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages will

# contain a <link> tag referring to it.  The value of this option must be the

# base URL from which the finished HTML is served.

#

# html_use_opensearch = ''

# -- Options for LaTeX output ------------------------------------------------

# This is the file name suffix for HTML files (e.g. ".xhtml").

# html_file_suffix = None

# Language to be used for generating the HTML full-text search index.

# Sphinx supports the following languages:

#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'

#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'

#

# html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.

# 'ja' uses this config value.

# 'zh' user can custom change `jieba` dictionary path.

#

# html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that

# implements a search results scorer. If empty, the default will be used.

#

# html_search_scorer = 'scorer.js'

# Output file base name for HTML help builder.

htmlhelp_basename = filename + 'doc'

# -- Options for LaTeX output ---------------------------------------------

latex_elements = {

     # The paper size ('letterpaper' or 'a4paper').

     # Additional stuff for the LaTeX preamble.

     #

'preamble': r'''

\usepackage{amssymb}

\newcommand{\DUrolecredits}{\footnotesize\color{lightgray}\newline}

''',

'preamble': '\usepackage{amssymb}',

     # Latex figure (float) alignment

     #

# latex_domain_indices = True

# -- Options for manual page output ------------------------------------------

# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples

# (source start file, name, description, authors, manual section).

# man_show_urls = False

# -- Options for Texinfo output ----------------------------------------------

# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples

# (source start file, target name, title, author,

# texinfo_no_detailmenu = False

# -- Options for Epub output -------------------------------------------------

# -- Options for Epub output ----------------------------------------------

# Bibliographic Dublin Core info.

epub_title = project

#

# epub_use_index = True

# -- Extension configurations ------------------------------------------------

# -- Options for todo extension ----------------------------------------------

# If true, `todo` and `todoList` produce output, else they produce nothing.

todo_include_todos = True

# Example configuration for intersphinx: refer to the Python standard library.

intersphinx_mapping = {'https://docs.python.org/': None}

# -- Options for pybtex ----------------------------------------------

from pybtex.style.formatting.unsrt import Style as UnsrtStyle, date, pages, toplevel

from pybtex.style.template import * # ... and anything else needed

from pybtex.plugin import register_plugin

class ADSArxivStyle(UnsrtStyle):

    def format_article(self, e):

        volume_and_pages = first_of [

            # volume and pages, with optional issue number

            optional [

                join [

                    field('volume'),

                    optional['(', field('number'),')'],

                    ':', pages

                ],

            ],

            # pages only

            words ['pages', pages],

        ]

        myurl = first_of [

                optional_field('adsurl'),

                join ['http://arxiv.org/abs/', optional_field('eprint')],

                optional_field('url'),

                optional [join ['http://dx.doi.org/', field('doi')]]

        ]

        template = toplevel [

            self.format_names('author'),

            href [myurl, self.format_title(e, 'title')] \

                if len(myurl.format_data(e)) > 0 \

                else tag('strong') [self.format_title(e, 'title')],

            sentence(capfirst=False) [

                tag('emph') [field('journal')],

                optional[ volume_and_pages ],

                field('year')],

            sentence(capfirst=False) [ optional_field('note') ],

        ]

        return template.format_data(e)

    def format_inproceedings(self, e):

        myurl = first_of [

                optional_field('adsurl'),

                optional [join ['http://arxiv.org/abs/', field('eprint')]],

                optional_field('url'),

                optional [join ['http://dx.doi.org/', field('doi')]]

        ]

        template = toplevel [

            sentence [self.format_names('author')],

            href [myurl, self.format_title(e, 'title')] \

                if len(myurl.format_data(e)) > 0 \

                else tag('strong') [self.format_title(e, 'title')],

            words [

                'In',

                sentence(capfirst=False) [

                    optional[ self.format_editor(e, as_sentence=False) ],

                    self.format_btitle(e, 'booktitle', as_sentence=False),

                    self.format_volume_and_series(e, as_sentence=False),

                    optional[ pages ],

                ],

                self.format_address_organization_publisher_date(e),

            ],

            sentence(capfirst=False) [ optional_field('note') ],

        ]

        return template.format_data(e)

# -- Options for pybtex ------------------------------------------------------

bibtex_bibfiles = ['references.bib']

register_plugin('pybtex.style.formatting', 'adsarxiv', ADSArxivStyle)

  {

   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' */

  sig = 10.0*nlevelsm1;

  sig1 = 1.0;

  medfac = prefs.back_pearsons;

  meafac = prefs.back_pearsons - 1.0;

  mea = med = bkg->mean;

  for (n=100; n-- && (sig>=0.1) && (fabs(sig/sig1-1.0)>EPS);)

    {

  *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;

*	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

*

*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/

  {"BACK_FILTERSIZE", P_INTLIST, prefs.backfsize, 1,11, 0.0,0.0,

    {""}, 1,2, &prefs.nbackfsize},

  {"BACK_FILTTHRESH", P_FLOAT, &prefs.backfthresh, 0,0, 0.0,BIG},

  {"BACK_PEARSONS", P_FLOAT, &prefs.back_pearsons, 0,0, 1.0,BIG},

  {"BACKPHOTO_THICK", P_INT, &prefs.pback_size, 1, 256},

  {"BACKPHOTO_TYPE", P_KEY, &prefs.pback_type, 0,0, 0.0,0.0,

   {"GLOBAL","LOCAL",""}},

" ",

"*BACK_TYPE        AUTO           # AUTO or MANUAL",

"*BACK_VALUE       0.0            # Default background value in MANUAL mode",

"*BACK_PEARSONS    2.5            # Pearson's factor P >= 1 with",

"*                                # (mean - mode) ~ P * (mean - median)",

"*                                # Legacy value is 2.5, but 3.5 is more accurate",

"BACK_SIZE        64             # Background mesh: <size> or <width>,<height>",

"BACK_FILTERSIZE  3              # Background filter: <size> or <width>,<height>",

" ",

*

*	This file part of:	SExtractor

*

*	Copyright:		(C) 1993-2020 IAP/CNRS/SorbonneU

*	Copyright:		(C) 1993-2023 IAP/CNRS/SorbonneU

*

*	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:		15/07/2020

*	Last modified:		07/03/2023

*

*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/

  int		backfsize[2];				/* bkgnd filt. size */

  int		nbackfsize;				/* nb of params */

  double	backfthresh;				/* bkgnd fil. thresh */

  double	back_pearsons;				/* Pearson's factor */

  enum	{GLOBAL, LOCAL}			pback_type;	/* phot. bkgnd type */

  int		pback_size;				/* rect. ann. width */

/*----- memory */