Merge branch 'Pearsons' into doc

configure.ac

@@ -7,7 +7,7 @@
 #
 #	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
 #
@@ -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:		26/02/2023
+#	Last modified:		07/03/2023
 #
 #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
@@ -31,7 +31,7 @@ define([AC_CACHE_LOAD],)
 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)

doc/src/conf.py

@@ -16,27 +16,32 @@
 # 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:
@@ -54,7 +59,7 @@ master_doc = 'index'
 # 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
@@ -62,9 +67,16 @@ author = u'E. Bertin'
 # 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:
@@ -78,7 +90,21 @@ today = 'Tue Mar 07 2023'
 # 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.
@@ -88,17 +114,53 @@ exclude_patterns = ['global.rst','keys.rst','macro.rst','roles.rst']
 # 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".
@@ -106,7 +168,49 @@ html_static_path = ['../theme']
 
 # 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.
 #
@@ -114,9 +218,39 @@ html_show_sphinx = False
 
 # 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 = ''
+
+# 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'
 
-# -- Options for LaTeX output ------------------------------------------------
+# 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').
@@ -129,10 +263,7 @@ latex_elements = {
 
      # Additional stuff for the LaTeX preamble.
      #
-'preamble': r'''
-\usepackage{amssymb}
-\newcommand{\DUrolecredits}{\footnotesize\color{lightgray}\newline}
-''',
+'preamble': '\usepackage{amssymb}',
 
      # Latex figure (float) alignment
      #
@@ -180,7 +311,7 @@ latex_show_urls = 'footnote'
 # 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).
@@ -194,7 +325,7 @@ man_pages = [
 # 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,
@@ -222,7 +353,7 @@ texinfo_documents = [
 # texinfo_no_detailmenu = False
 
 
-# -- Options for Epub output -------------------------------------------------
+# -- Options for Epub output ----------------------------------------------
 
 # Bibliographic Dublin Core info.
 epub_title = project
@@ -306,13 +437,74 @@ epub_exclude_files = ['search.html']
 #
 # 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
 
-# -- Options for pybtex ------------------------------------------------------
-bibtex_bibfiles = ['references.bib']
+# 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)
+
+register_plugin('pybtex.style.formatting', 'adsarxiv', ADSArxivStyle)
 

src/back.c

@@ -673,7 +673,7 @@ float	backguess(backstruct *bkg, float *mean, float *sigma)
   {
    LONG		*histo, *hilow, *hihigh, *histot;
    unsigned long lowsum, highsum, sum;
-   double	ftemp, mea, sig, sig1, med, dpix;
+   double	ftemp, mea,meafac, sig, sig1, med,medfac, dpix;
    int		i, n, lcut,hcut, nlevelsm1, pix;
 
 /* Leave here if the mesh is already classified as `bad' */
@@ -689,6 +689,8 @@ float	backguess(backstruct *bkg, float *mean, float *sigma)
 
   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);)
     {
@@ -725,7 +727,7 @@ float	backguess(backstruct *bkg, float *mean, float *sigma)
   *mean = fabs(sig)>0.0? (fabs(bkg->sigma/(sig*bkg->qscale)-1) < 0.0 ?
 			    bkg->qzero+mea*bkg->qscale
 			    :(fabs((mea-med)/sig)< 0.3 ?
-			      bkg->qzero+(2.5*med-1.5*mea)*bkg->qscale
+			      bkg->qzero+(medfac*med - meafac*mea)*bkg->qscale
 			     :bkg->qzero+med*bkg->qscale))
                        :bkg->qzero+mea*bkg->qscale;
 

src/preflist.h

@@ -22,7 +22,7 @@
 *	You should have received a copy of the GNU General Public License
 *	along with SExtractor. If not, see <http://www.gnu.org/licenses/>.
 *
-*	Last modified:		15/07/2020
+*	Last modified:		07/03/2023
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -61,6 +61,7 @@
   {"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",""}},
@@ -261,6 +262,9 @@ char *default_prefs[] =
 " ",
 "*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>",
 " ",

src/prefs.h

@@ -7,7 +7,7 @@
 *
 *	This file part of:	SExtractor
 *
-*	Copyright:		(C) 1993-2020 IAP/CNRS/SorbonneU
+*	Copyright:		(C) 1993-2023 IAP/CNRS/SorbonneU
 *
 *	License:		GNU General Public License
 *
@@ -22,7 +22,7 @@
 *	You should have received a copy of the GNU General Public License
 *	along with SExtractor. If not, see <http://www.gnu.org/licenses/>.
 *
-*	Last modified:		15/07/2020
+*	Last modified:		07/03/2023
 *
 *%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
@@ -136,6 +136,7 @@ typedef struct
   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 */