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Commit 40833b3b authored by Emmanuel Bertin's avatar Emmanuel Bertin
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Merge branch 'Pearsons' into doc

parents 1a9b70b3 f66d6f79
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configure.ac
View file @ 40833b3b
......@@ -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
View file @ 40833b3b
......@@ -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
View file @ 40833b3b
......@@ -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
View file @ 40833b3b
......@@ -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
View file @ 40833b3b
......@@ -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 */
......
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