diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml
new file mode 100644
index 0000000000000000000000000000000000000000..d7ebf1eca96e144055abc8180cf5febd63afeb5a
--- /dev/null
+++ b/.github/workflows/doc.yml
@@ -0,0 +1,54 @@
+name: doc
+
+on:
+ push:
+ paths:
+ - 'doc/**'
+ pull_request:
+ paths:
+ - 'doc/**'
+ workflow_dispatch:
+
+jobs:
+
+#############
+# Build doc #
+#############
+ build:
+ name: Make doc
+ continue-on-error: false
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v2
+
+ - name: Install dependencies
+ run: |
+ pip3 install -r doc/requirements.txt
+ sudo apt-get -y install latexmk texlive-latex-recommended texlive-fonts-recommended texlive-formats-extra
+
+ - name: Build doc
+ run: |
+ ./autogen.sh
+ ./configure --disable-model-fitting --disable-cfitsio --disable-threads
+ cd doc
+ make html
+ make latexpdf
+ cp build/latex/sextractor.pdf build/html/
+
+ - name: Set destination dir
+ if: github.ref_name != 'main'
+ run: |
+ echo "DOC_DEST=${{ github.ref_name }}" >> $GITHUB_ENV
+
+ - name: Deploy
+ if: success()
+ uses: peaceiris/actions-gh-pages@v3
+ with:
+ publish_branch: doc-pages
+ github_token: ${{ secrets.GITHUB_TOKEN }}
+ publish_dir: doc/build/html/
+ destination_dir: ${{ env.DOC_DEST }}
+
+
diff --git a/INSTALL b/INSTALL
index 43c1ed1a01aadb4ea8e870158512a8bf90d5831b..32aed6e476335054c5103dea35d4a4fb442da369 100644
--- a/INSTALL
+++ b/INSTALL
@@ -4,7 +4,7 @@ Installing the software
Hardware requirements
=====================
-PSFEx runs in (ANSI) text-mode from a shell. A window system is
+SExtractor 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
@@ -75,18 +75,19 @@ 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
+Intel compiler ("icc" or "icx") 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" (or "icx") 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
+machine that does not have "icc" (or "icx") and the MKL 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
@@ -118,6 +119,5 @@ path).
options "--enable-threads --enable-float".
[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.
+ Kernel Library) are now available for free on Intel's website.
diff --git a/configure.ac b/configure.ac
index 433b6e52f279b69e61090422aac58ddf04b3d32e..07e1b374d6209c980fb54da49e3dfe6927f271fe 100644
--- a/configure.ac
+++ b/configure.ac
@@ -7,7 +7,7 @@
#
# This file part of: SExtractor
#
-# Copyright: (C) 2002-2022 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 .
#
-# Last modified: 11/03/2022
+# Last modified: 07/03/2023
#
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -31,8 +31,8 @@ define([AC_CACHE_LOAD],)
define([AC_CACHE_SAVE],)
# This is your standard AstrOmatic source code...
-AC_INIT(SExtractor, 2.25.3, [astromatic@astromatic.net],
- sextractor, [http://astromatic.net/software/sextractor])
+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)
AC_CONFIG_SRCDIR(src/makeit.c)
@@ -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)
@@ -79,24 +80,38 @@ AC_ARG_ENABLE(auto-flags,
AC_MSG_RESULT([yes]),
AC_MSG_RESULT([no]))
-# Provide special option for the Linux Intel C compiler
-AC_MSG_CHECKING([whether the INTEL compiler is enabled])
+# Provide special option for the Linux Intel C "classic" compiler
+AC_MSG_CHECKING([whether the classic INTEL compiler is enabled])
AC_ARG_ENABLE(icc,
[AS_HELP_STRING([--enable-icc],
[Use the Intel compiler (default = no)])],
CC="icc"
+ enable_iccx="yes"
+ AC_MSG_RESULT([yes]),
+ AC_MSG_RESULT([no]))
+
+# Provide special option for the Linux Intel OneAPI C compiler
+AC_MSG_CHECKING([whether the INTEL compiler is enabled])
+AC_ARG_ENABLE(icx,
+ [AS_HELP_STRING([--enable-icx],
+ [Use the Intel compiler (default = no)])],
+ CC="icx"
+ enable_iccx="yes"
AC_MSG_RESULT([yes]),
AC_MSG_RESULT([no]))
# Provide special options for INTEL MKL
-# We force the use of icc
+# We use icc if available, if not Intel OneAPI's icx
+# (we don't use AC_PROG_CC as it does not play nice
+# in a conditional block)
AC_MSG_CHECKING([whether INTEL's MKL is enabled])
AC_ARG_ENABLE(mkl,
[AS_HELP_STRING([--enable-mkl],
[Use INTEL's MKL for solvers and FFTs (default = no)])],
- enable_icc="yes"
- CC="icc"
- AC_MSG_RESULT([yes]),
+ AC_MSG_RESULT([yes])
+ CC=""
+ [AC_CHECK_PROGS(CC, [icc icx cc])]
+ enable_iccx="yes",
AC_MSG_RESULT([no]))
# Checks for programs.
@@ -115,11 +130,10 @@ AC_PROG_INSTALL
AC_CHECK_LIB(m, sin)
# Checks for header files.
-AC_HEADER_STDC
AC_CHECK_HEADERS([fcntl.h limits.h malloc.h stdlib.h string.h sys/mman.h \
sys/types.h unistd.h])
# Checks for INTEL math header files.
-if test "$enable_icc" = "yes"; then
+if test "$enable_iccx" = "yes"; then
AC_CHECK_HEADERS(mathimf.h)
fi
@@ -135,7 +149,6 @@ AC_TYPE_UID_T
# Checks for library functions.
AC_FUNC_ERROR_AT_LINE
AC_FUNC_MMAP
-AC_TYPE_SIGNAL
AC_FUNC_STAT
AC_FUNC_STRFTIME
AC_CHECK_FUNCS([atexit getenv gettimeofday isinf isnan logf memcpy memmove \
@@ -180,6 +193,24 @@ AC_ARG_WITH(openblas-incdir,
[AS_HELP_STRING([--with-openblas-incdir=],
[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 "$enable_cfitsio" = "no"; then
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi,
+ AC_MSG_RESULT([no]))
+AC_ARG_WITH(cfitsio-libdir,
+ [AS_HELP_STRING([--with-cfitsio-libdir=],
+ [Provide an alternative path to the CFITSIO library])])
+AC_ARG_WITH(cfitsio-incdir,
+ [AS_HELP_STRING([--with-cfitsio-incdir=],
+ [Provide an alternative path to the CFITSIO include directory])])
+
# Provide a special option for the default XSLT URL
with_xsl_url="file://"$(URBI_RESOLVE_DIR([$datadir]))"/$PACKAGE_TARNAME/$PACKAGE_TARNAME.xsl"
AC_ARG_WITH(xsl_url,
@@ -222,7 +253,7 @@ use_pthreads="no"
AC_MSG_CHECKING([for profiler mode])
AC_ARG_ENABLE(profiling,
[AS_HELP_STRING([--enable-profiling],
- [Enable special mode for profiling (default = no)])]
+ [Enable special mode for profiling (default = no)])],
AC_MSG_RESULT([yes]),
AC_MSG_RESULT([no]))
@@ -256,10 +287,7 @@ if test "$enable_model_fitting" != "no"; then
if test "$enable_mkl" = "yes"; then
convlibs="${srcdir}/wcs/libwcs_c.a,${srcdir}/levmar/liblevmar.a"
ACX_MKL($with_mkl_dir,,$enable_best_link,$convlibs)
- if test "$MKL_WARN" == ""; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
+ if test "$MKL_WARN" != ""; then
AC_MSG_WARN([$MKL_WARN])
fi
AM_CFLAGS="$AM_CFLAGS $MKL_CFLAGS "
@@ -305,11 +333,21 @@ if test "$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 "$enable_model_fitting" != "no"])
# Compile with profiling option
if test "$enable_profiling" = "yes"; then
- if test "$enable_icc" = "yes"; then
+ if test "$enable_iccx" = "yes"; then
AM_CFLAGS="$AM_CFLAGS -pq"
else
AM_CFLAGS="$AM_CFLAGS -pg"
@@ -319,9 +357,9 @@ fi
# "Best" linking option
if test "$enable_best_link" = "yes"; then
- if test "$enable_icc" = "yes"; then
- AM_LDFLAGS="-static-intel -qopenmp-link static -shared-libgcc \
- -static-libtool-libs -no-intel-extensions -avoid-version $AM_LDFLAGS"
+ if test "$enable_iccx" = "yes"; then
+ AM_LDFLAGS="-static-intel -qopenmp-link=static -shared-libgcc \
+ -static-libtool-libs -avoid-version $AM_LDFLAGS"
else
AM_LDFLAGS="-shared-libgcc -static-libtool-libs -avoid-version $AM_LDFLAGS"
fi
diff --git a/debian/rules b/debian/rules
index a4e2ad655553efc81df5d4941e156f1e75d62f31..2033ae254b2407a74f2f118dc1387b63ab8d1145 100755
--- a/debian/rules
+++ b/debian/rules
@@ -15,7 +15,7 @@ ifeq ($(USE_BEST),1)
dh_auto_configure -- --host=$(DEB_HOST_GNU_TYPE) \
--build=$(DEB_BUILD_GNU_TYPE) \
--prefix=/usr --mandir=\$${prefix}/share/man \
- --enable-icc --enable-mkl \
+ --enable-icx --enable-mkl \
--enable-auto-flags --enable-best-link \
--with-release=$(PACKAGE_RELEASE)
else
diff --git a/doc/requirements.txt b/doc/requirements.txt
index ef36addc628cc318f4bd7e62a2a4a62827230a49..f73d568ad7ebe2de2b397348ec42fa32cb44d0b9 100644
--- a/doc/requirements.txt
+++ b/doc/requirements.txt
@@ -1 +1,4 @@
-sphinxcontrib-bibtex
+sphinx >= 5.0
+sphinx_rtd_theme >= 1.1
+sphinxcontrib-bibtex >= 2.4.0
+
diff --git a/doc/src/Background.rst b/doc/src/Background.rst
index cfaa7da65a80a0e7055113b3c4ea858eff138a37..bf5df53f6f4611ba5ef60f23723c919eb9d96bef 100644
--- a/doc/src/Background.rst
+++ b/doc/src/Background.rst
@@ -18,19 +18,26 @@ Background estimation
To compute the background map, |SExtractor| makes a first pass through the pixel data, estimating the local background in each mesh of a rectangular grid that covers the whole frame.
The background estimator is a combination of :math:`\kappa\,\sigma` clipping and mode estimation, similar to Stetson’s |DAOPHOT|_ program :cite:`1987PASP_99_191S,1992ASPC_23_90D`.
-Briefly, the local background histogram is clipped iteratively until convergence at :math:`\pm 3\sigma` around its median. The mode of the histogram is estimated using:
+Briefly, the local background histogram is clipped iteratively until convergence at :math:`\pm 3\sigma` around its median. The mode of the histogram is estimated using the semi-empirical relation
.. math::
- :label: sexbackmode
+ :label: ksbackmode
- \mbox{Mode} = 2.5 \times \mbox{Median} - 1.5 \times \mbox{Mean}.
+ \mbox{Mode} - \mbox{Mean} \approx \alpha_{\rm{Pearson}} \times (\mbox{Median} - \mbox{Mean}),
-Using simulated images, the expression above was found more accurate with clipped distributions :cite:`1996AAS_117_393B` than the usual approximation (e.g., :cite:`stuart2009kendall`):
+and therefore
.. math::
- :label: ksbackmode
+ :label: sexbackmode
+
+ \mbox{Mode} \approx \alpha_{\rm{Pearson}} \times \mbox{Median} - (\alpha_{\rm{Pearson}} - 1) \times \mbox{Mean},
+
+with :math:`\alpha_{\rm{Pearson}} \approx 3` :cite:`1895RSTA_0010,1911AITS,stuart2009kendall`.
- \mbox{Mode} = 3 \times \mbox{Median} - 2 \times \mbox{Mean}.
+Using simulated images, :cite:`1996AAS_117_393B` found :math:`\alpha_{\rm{Pearson}} \approx 2.5` more appropriate for determining the mode of the background histogram in |SExtractor|.
+However, extensive photometric assessments carried out in the context of the `Dark Energy Survey `_ later showed that this value leads to a slight overestimation of the local background :cite:`2022ApJS_258_15E`, and a higher :math:`\alpha_{\rm{Pearson}} \approx 3.5` was adopted in |DES|.
+Since |SExtractor| v2.28, :math:`\alpha_{\rm{Pearson}}` can be changed using the ``BACK_PEARSON`` configuration parameter.
+However, for the sake of compatibility with previous results, the default value of ``BACK_PEARSON`` remains ``2.5``.
:numref:`fig_modevsmean` shows that the mode estimation in :eq:`sexbackmode` is considerably less affected by source crowding than a simple clipped mean :cite:`1981AJ_86_476J,1987AA_183_177I` but it is :math:`\approx 30\%` noisier.
Obviously :eq:`sexbackmode` is not valid for any distribution; |SExtractor| falls back to a simple median for estimating the local background value if the mode and the median disagree by more than 30%.
@@ -56,7 +63,7 @@ In parallel with the making of the background map, an *RMS background map*, that
It may be used as an internal weight map if the ``WEIGHT_TYPE`` configuration parameter is to ``BACKGROUND`` (see :ref:`weight-map_format`).
Configuration and tuning
-------------------------
+~~~~~~~~~~~~~~~~~~~~~~~~
.. note::
All background configuration parameters also affect background-RMS maps.
diff --git a/doc/src/Model.rst b/doc/src/Model.rst
index 160c943de7a351dd639b280d8e31a856684a3fd2..b2ac587fb6c75dd76bc820e551ab7afc9e61c9e0 100644
--- a/doc/src/Model.rst
+++ b/doc/src/Model.rst
@@ -269,7 +269,7 @@ Model-based star-galaxy separation: :param:`SPREAD_MODEL`
---------------------------------------------------------
The :param:`SPREAD_MODEL` estimator has been developed as a star/galaxy classifier for the DESDM pipeline :cite:`2012SPIE_8451E_0DM`, and has also been used in other surveys :cite:`2012ApJ_757_83D,2013AA_554A_101B`.
-:param:`SPREAD_MODEL` indicates which of the best fitting local PSF model resampled at the current position :math:`\tilde{\boldsymbol{\phi}}` (representing a point source) or a slightly ``fuzzier'' resampled model :math:`\tilde{\boldsymbol{G}}` (representing a galaxy) matches best the image data.
+:param:`SPREAD_MODEL` indicates which of the best fitting local PSF model resampled at the current position :math:`\tilde{\boldsymbol{\phi}}` (representing a point source) or a slightly "fuzzier" resampled model :math:`\tilde{\boldsymbol{G}}` (representing a galaxy) matches best the image data.
:math:`\tilde{\boldsymbol{G}}` is obtained by convolving the local PSF model with a circular exponential model with scalelength = 1/16 |FWHM|, and resampling the result at the current position on the pixel grid. :param:`SPREAD_MODEL` is normalized to allow comparing sources with different PSFs throughout the field:
.. math::
@@ -306,6 +306,7 @@ In order to maintain a certain level of purity or completeness across the whole
.. math::
:label: spreaderr_model
+ :nowrap:
\begin{eqnarray}
{\tt SPREADERR\_MODEL} & = & \frac{1}{(\tilde{\boldsymbol{\phi}}^\mathsf{T} {\bf W}\,\boldsymbol{p})^2} \left((\tilde{\boldsymbol{G}}^\mathsf{T} {\bf V}\,\tilde{\boldsymbol{G}})\,(\tilde{\boldsymbol{\phi}}^\mathsf{T} {\bf W}\,\boldsymbol{p})^2\right.\nonumber \\
diff --git a/doc/src/Position.rst b/doc/src/Position.rst
index a91d5ade89a75080caa6e98eca7ea0d5941fa241..964d4e824f077fea1c712172716be7ba1dc0e249 100644
--- a/doc/src/Position.rst
+++ b/doc/src/Position.rst
@@ -27,6 +27,7 @@ These coordinates define two corners of a rectangle which encloses the detected
.. math::
:label: xminymax
+ :nowrap:
\begin{eqnarray}
{\tt XMIN} & = & \min_{i \in {\cal S}} x_i,\\
@@ -47,6 +48,7 @@ Barycenter coordinates generally define the position of the “center” of a so
.. math::
:label: xy
+ :nowrap:
\begin{eqnarray}
{\tt X} & = & \overline{x} = \frac{\displaystyle \sum_{i \in {\cal S}}
@@ -76,6 +78,7 @@ Second-order moments: :param:`X2`, :param:`Y2`, :param:`XY`
.. math::
:label: x2y2
+ :nowrap:
\begin{eqnarray}
{\tt X2} & = \overline{x^2} = & \frac{\displaystyle \sum_{i \in {\cal S}} p^{(f)}_i x_i^2}{\displaystyle \sum_{i \in {\cal S}} p^{(f)}_i} - \overline{x}^2,\\
@@ -144,6 +147,7 @@ covariance :math:`\overline{xy}`.
.. math::
:label: aimage
+ :nowrap:
\begin{eqnarray}
{\tt A}^2 & = & \overline{x^2}_{\tt THETA},\ \ \ {\rm and}\\
@@ -154,6 +158,7 @@ covariance :math:`\overline{xy}`.
.. math::
:label: aimage_2
+ :nowrap:
\begin{eqnarray}
{\tt A}^2 & = & \frac{\overline{x^2}+\overline{y^2}}{2}
@@ -175,6 +180,7 @@ These parameters [#elongation]_ are directly derived from :param:`A` and :param:
.. math::
:label: elongation
+ :nowrap:
\begin{eqnarray}
{\tt ELONGATION} & = & \frac{\tt A}{\tt B}\ \ \ \ \ \mbox{and}\\
@@ -206,6 +212,7 @@ parameters can be derived from the 2nd order moments:
.. math::
:label: ellipse_2
+ :nowrap:
\begin{eqnarray}
{\tt CXX} & = & \frac{\cos^2 {\tt THETA}}{{\tt A}^2} + \frac{\sin^2
@@ -240,6 +247,7 @@ Furthermore, |SExtractor| does not currently take into account possible correlat
.. math::
:label: errxy
+ :nowrap:
\begin{eqnarray}
{\tt ERRX2} & = {\rm var}(\overline{x}) =
@@ -261,6 +269,7 @@ where :math:`{\sigma_B}_i` is the local background noise and :math:`g_i` the loc
.. math::
:label: errabtheta
+ :nowrap:
\begin{eqnarray}
{\tt ERRA}^2 & = & \frac{{\rm var}(\overline{x})+{\rm var}(\overline{y})}{2}
@@ -277,6 +286,7 @@ And the error ellipse parameters are:
.. math::
:label: errellipse
+ :nowrap:
\begin{eqnarray}
{\tt ERRCXX} & = & \frac{\cos^2 {\tt ERRTHETA}}{{\tt ERRA}^2} +
diff --git a/doc/src/adsarxiv.py b/doc/src/adsarxiv.py
new file mode 100644
index 0000000000000000000000000000000000000000..251f82b54d150dfa2bf7760256c65c2066b8a6a7
--- /dev/null
+++ b/doc/src/adsarxiv.py
@@ -0,0 +1,221 @@
+"""
+ADSArxiv PybTeX style
+"""
+# Copyright Emmanuel Bertin CFHT/CNRS/SorbonneU
+# Licensed under GPL v3
+
+from packaging import version as vers
+from pybtex import __version__ as pybtex_version
+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
+
+pybtex_new_version = vers.parse(pybtex_version) >= vers.parse("0.22")
+
+if pybtex_new_version:
+ def _format_data(node, data):
+ try:
+ f = node.format_data
+ except AttributeError:
+ return node
+ else:
+ return f(data)
+
+
+ def _format_list(list_, data):
+ return (_format_data(part, data) for part in list_)
+
+ @node
+ def href2(children, data):
+ parts = _format_list(children, data)
+ if "http" in list(parts)[0]:
+ parts = _format_list(children, data)
+ return richtext.HRef(*parts)
+ else:
+ parts = _format_list(children, data)
+ return richtext.Tag('strong', *parts)
+
+class ADSArxivStyle(UnsrtStyle):
+
+ if pybtex_new_version:
+ def format_names(self, role, as_sentence=True):
+ formatted_names = names(role, sep=', ', sep2 = ' and ', last_sep=', and ')
+ if as_sentence:
+ return sentence[ formatted_names ]
+ else:
+ return formatted_names
+
+ def get_article_template(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'),
+ 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', as_sentence=False), field('year') ],
+ href2[ myurl, self.format_title(e, 'title') ],
+ sentence(capfirst=False) [
+ tag('emph')[ field('journal') ],
+ optional[ volume_and_pages ]],
+ sentence(capfirst=False) [ optional_field('note') ],
+ ]
+ return template
+
+ def get_book_template(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[
+ self.format_author_or_editor(e),
+ href2[ myurl, self.format_btitle(e, 'title') ],
+ self.format_volume_and_series(e),
+ sentence [
+ field('publisher'),
+ optional_field('address'),
+ self.format_edition(e),
+ date
+ ],
+ optional[ sentence [ self.format_isbn(e) ] ],
+ sentence [ optional_field('note') ],
+ ]
+ return template
+
+ def get_inproceedings_template(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', as_sentence=False), field('year') ],
+ href2[ myurl, 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
+
+ def get_misc_template(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[
+ optional[ sentence[ self.format_names('author', as_sentence=False), optional [ field('year') ]]],
+ optional[ href2[ myurl, self.format_title(e, 'title') ]],
+ sentence[ optional[ field('howpublished') ]],
+ sentence[ optional_field('note') ],
+ ]
+ return template
+ else:
+
+ 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'),
+ optional [join ['http://arxiv.org/abs/'], 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')],
+ 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_book(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 [
+ self.format_author_or_editor(e),
+ href [myurl, self.format_btitle(e, 'title')] \
+ if len(myurl.format_data(e)) > 0 \
+ else tag('strong') [self.format_btitle(e, 'title')],
+ self.format_volume_and_series(e),
+ sentence [
+ field('publisher'),
+ optional_field('address'),
+ self.format_edition(e),
+ date
+ ],
+ optional[ sentence [ self.format_isbn(e) ] ],
+ 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)
+
diff --git a/doc/src/conf.py b/doc/src/conf.py
deleted file mode 100644
index f41e8807ad36df983cb5ccad80e5afca579e6806..0000000000000000000000000000000000000000
--- a/doc/src/conf.py
+++ /dev/null
@@ -1,510 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# SExtractor documentation build configuration file, created by
-# sphinx-quickstart on Tue Sep 27 15:11:21 2016.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# 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
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-import sphinx_rtd_theme
-
-
-# -- 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 = [
-# 'sphinx.ext.intersphinx',
-# 'sphinx.ext.todo',
- 'sphinx.ext.mathjax',
- 'sphinxcontrib.bibtex',
- 'sphinx.ext.githubpages'
-]
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The encoding of source files.
-#
-# source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'SExtractor'
-filename = 'sextractor'
-copyright = u'2017, IAP/CNRS/UPMC'
-author = u'E. Bertin'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '2.25.3'
-# The full version, including alpha/beta/rc tags.
-release = '2.25.3'
-
-# 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:
-#
-today = 'Fri Mar 11 2022'
-#
-# Else, today_fmt is used as the format for a strftime call.
-#
-# today_fmt = '%B %d, %Y'
-
-# 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','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.
-#
-# show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# 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
-
-numfig = True
-
-# -- 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.
-# " v documentation" by default.
-#
-# html_title = u'SExtractor v2.25.3'
-
-# 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".
-html_static_path = ['../theme']
-
-# Trick for having ReadTheDocs read custom theme changes
-def setup(app):
- 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.
-#
-html_show_sphinx = False
-
-# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#
-# html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a 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'
-
-# 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').
- #
-'papersize': 'a4paper',
-
- # The font size ('10pt', '11pt' or '12pt').
- #
- # 'pointsize': '10pt',
-
- # Additional stuff for the LaTeX preamble.
- #
-'preamble': '\usepackage{amssymb}',
-
- # Latex figure (float) alignment
- #
- # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-# author, documentclass [howto, manual, or own class]).
-latex_documents = [
- (master_doc, filename + '.tex', project + u' Documentation',
- author, 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#
-# latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#
-# latex_use_parts = False
-
-# If true, show page references after internal links.
-#
-# latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-#
-latex_show_urls = 'footnote'
-
-# Documents to append as an appendix to all manuals.
-#
-# latex_appendices = []
-
-# It false, will not define \strong, \code, itleref, \crossref ... but only
-# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
-# packages.
-#
-# latex_keep_old_macro_names = True
-
-# If false, no module index is generated.
-#
-# latex_domain_indices = True
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
- (master_doc, filename, project + u' Documentation',
- author, 1)
-]
-
-# If true, show URL addresses after external links.
-#
-# man_show_urls = False
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-# dir menu entry, description, category)
-texinfo_documents = [
- (master_doc, filename, project + u' Documentation',
- author, project, 'One line description of project.',
- 'Miscellaneous'),
-]
-
-# Documents to append as an appendix to all manuals.
-#
-# texinfo_appendices = []
-
-# If false, no module index is generated.
-#
-# texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#
-# texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-#
-# texinfo_no_detailmenu = False
-
-
-# -- Options for Epub output ----------------------------------------------
-
-# Bibliographic Dublin Core info.
-epub_title = project
-epub_author = author
-epub_publisher = author
-epub_copyright = copyright
-
-# The basename for the epub file. It defaults to the project name.
-# epub_basename = project
-
-# The HTML theme for the epub output. Since the default themes are not
-# optimized for small screen space, using the same theme for HTML and epub
-# output is usually not wise. This defaults to 'epub', a theme designed to save
-# visual space.
-#
-# epub_theme = 'epub'
-
-# The language of the text. It defaults to the language option
-# or 'en' if the language is not set.
-#
-# epub_language = ''
-
-# The scheme of the identifier. Typical schemes are ISBN or URL.
-# epub_scheme = ''
-
-# The unique identifier of the text. This can be a ISBN number
-# or the project homepage.
-#
-# epub_identifier = ''
-
-# A unique identification for the text.
-#
-# epub_uid = ''
-
-# A tuple containing the cover image and cover page html template filenames.
-#
-# epub_cover = ()
-
-# A sequence of (type, uri, title) tuples for the guide element of content.opf.
-#
-# epub_guide = ()
-
-# HTML files that should be inserted before the pages created by sphinx.
-# The format is a list of tuples containing the path and title.
-#
-# epub_pre_files = []
-
-# HTML files that should be inserted after the pages created by sphinx.
-# The format is a list of tuples containing the path and title.
-#
-# epub_post_files = []
-
-# A list of files that should not be packed into the epub file.
-epub_exclude_files = ['search.html']
-
-# The depth of the table of contents in toc.ncx.
-#
-# epub_tocdepth = 3
-
-# Allow duplicate toc entries.
-#
-# epub_tocdup = True
-
-# Choose between 'default' and 'includehidden'.
-#
-# epub_tocscope = 'default'
-
-# Fix unsupported image types using the Pillow.
-#
-# epub_fix_images = False
-
-# Scale large images.
-#
-# epub_max_image_width = 0
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-#
-# epub_show_urls = 'inline'
-
-# If false, no index is generated.
-#
-# epub_use_index = 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)
-
-register_plugin('pybtex.style.formatting', 'adsarxiv', ADSArxivStyle)
-
diff --git a/doc/src/conf.py.in b/doc/src/conf.py.in
index 63ff40d4727bb0702d1de05bc7942232e41bb92b..d48e841e82043955941a3a35df78fbed34972701 100644
--- a/doc/src/conf.py.in
+++ b/doc/src/conf.py.in
@@ -16,32 +16,27 @@
# 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
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os, sys
+sys.path.insert(0, os.path.abspath('.'))
import sphinx_rtd_theme
+import adsarxiv
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
+# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
-# 'sphinx.ext.intersphinx',
-# 'sphinx.ext.todo',
- 'sphinx.ext.mathjax',
'sphinxcontrib.bibtex',
- 'sphinx.ext.githubpages'
+ 'sphinx.ext.githubpages',
+ 'sphinx.ext.mathjax',
+ 'sphinx.ext.todo',
]
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ['../theme']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
@@ -59,7 +54,7 @@ master_doc = 'index'
# General information about the project.
project = u'@PACKAGE_NAME@'
filename = '@PACKAGE_TARNAME@'
-copyright = u'2017, IAP/CNRS/UPMC'
+copyright = u'2017-2023, CFHT/IAP/CNRS/SorbonneU'
author = u'E. Bertin'
# The version info for the project you're documenting, acts as replacement for
@@ -71,13 +66,6 @@ version = '@PACKAGE_VERSION@'
# The full version, including alpha/beta/rc tags.
release = '@PACKAGE_VERSION@'
-# 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:
#
@@ -90,21 +78,7 @@ today = '@DATE2@'
# 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','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
+exclude_patterns = ['global.rst','keys.rst','macro.rst','roles.rst']
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
@@ -114,53 +88,17 @@ exclude_patterns = ['global.rst','keys.rst','roles.rst']
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
-# 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
-
numfig = True
-# -- Options for HTML output ----------------------------------------------
+smartquotes = False
+
+# -- 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.
-# " v documentation" by default.
-#
-# html_title = u'@PACKAGE_NAME@ v@PACKAGE_VERSION@'
-
-# 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".
@@ -168,49 +106,7 @@ html_static_path = ['../theme']
# Trick for having ReadTheDocs read custom theme changes
def setup(app):
- 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
+ app.add_css_file("css/custom.css")
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
@@ -218,39 +114,11 @@ 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
+html_logo = 'figures/cover.png'
+html_favicon = '../theme/images/astromaticO.png'
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a 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'
-
-# 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 ---------------------------------------------
+# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
@@ -263,11 +131,11 @@ latex_elements = {
# Additional stuff for the LaTeX preamble.
#
-'preamble': '\usepackage{amssymb}',
-
- # Latex figure (float) alignment
- #
- # 'figure_align': 'htbp',
+'preamble': r'''
+\usepackage{amssymb}
+\newcommand{\DUrolecredits}{\footnotesize\color{lightgray}\newline}
+\usepackage{etoolbox}
+\AtBeginEnvironment{figure}{\pretocmd{\hyperlink}{\protect}{}{}}'''
}
# Grouping the document tree into LaTeX files. List of tuples
@@ -281,7 +149,7 @@ latex_documents = [
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
-# latex_logo = None
+latex_logo = 'figures/cover.pdf'
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
@@ -294,7 +162,7 @@ latex_documents = [
# If true, show URL addresses after external links.
#
-latex_show_urls = 'footnote'
+# latex_show_urls = False
# Documents to append as an appendix to all manuals.
#
@@ -311,7 +179,7 @@ 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).
@@ -325,7 +193,7 @@ 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,
@@ -353,7 +221,7 @@ texinfo_documents = [
# texinfo_no_detailmenu = False
-# -- Options for Epub output ----------------------------------------------
+# -- Options for Epub output -------------------------------------------------
# Bibliographic Dublin Core info.
epub_title = project
@@ -437,74 +305,13 @@ 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
-# 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)
+# -- Options for pybtex ------------------------------------------------------
+bibtex_bibfiles = ['references.bib']
diff --git a/doc/src/figures/cover.pdf b/doc/src/figures/cover.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..a79998ae01d2ef911f460ff0f926b398c9322fa2
Binary files /dev/null and b/doc/src/figures/cover.pdf differ
diff --git a/doc/src/figures/cover.png b/doc/src/figures/cover.png
new file mode 100644
index 0000000000000000000000000000000000000000..ddbae731ea483422128565614c180c57c6a81d37
Binary files /dev/null and b/doc/src/figures/cover.png differ
diff --git a/doc/src/index.rst b/doc/src/index.rst
index 3f13d5addbeca1c186515637a3ea821b0050fc2f..ecfa234856a32a266b43701e13cf54324da36e3b 100644
--- a/doc/src/index.rst
+++ b/doc/src/index.rst
@@ -21,10 +21,3 @@ Contents
Measurements
references
-Indices and tables
-------------------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
diff --git a/doc/src/keys.rst b/doc/src/keys.rst
index fe3aa9581affc3b1754095c413268d6caa1c4c27..afe54b4f588bb6c538ce61dea00d15a5e9bca425 100644
--- a/doc/src/keys.rst
+++ b/doc/src/keys.rst
@@ -7,6 +7,9 @@
.. |DAOPHOT| replace:: :program:`DAOPHOT`
.. _DAOPHOT: http://ascl.net/phpBB3/viewtopic.php?t=23410
+.. |DES| replace:: :abbr:`Dark Energy Survey`
+.. _DES: https://darkenergysurvey.org
+
.. |.dmg| replace:: :file:`.dmg`
.. _.dmg: https://en.wikipedia.org/wiki/Apple_Disk_Image
diff --git a/doc/src/references.bib b/doc/src/references.bib
index ddebffb59fee7f068b030355410cc98f1877de37..e927626fe96db2e2d6cc93a3d1dca1c7e9c70271 100644
--- a/doc/src/references.bib
+++ b/doc/src/references.bib
@@ -141,6 +141,26 @@ archivePrefix = "arXiv",
pages = {1016-1022},
doi = {10.1175/1520-0450(1979)018<1016:LFIOAT>2.0.CO;2},
}
+
+@ARTICLE{2022ApJS_258_15E,
+ author = {{Everett}, S. and {Yanny}, B. and {Kuropatkin}, N. and {Huff}, E.~M. and {Zhang}, Y. and {Myles}, J. and {Masegian}, A. and {Elvin-Poole}, J. and {Allam}, S. and {Bernstein}, G.~M. and {Sevilla-Noarbe}, I. and {Splettstoesser}, M. and {Sheldon}, E. and {Jarvis}, M. and {Amon}, A. and {Harrison}, I. and {Choi}, A. and {Hartley}, W.~G. and {Alarcon}, A. and {S{\'a}nchez}, C. and {Gruen}, D. and {Eckert}, K. and {Prat}, J. and {Tabbutt}, M. and {Busti}, V. and {Becker}, M.~R. and {MacCrann}, N. and {Diehl}, H.~T. and {Tucker}, D.~L. and {Bertin}, E. and {Jeltema}, T. and {Drlica-Wagner}, A. and {Gruendl}, R.~A. and {Bechtol}, K. and {Carnero Rosell}, A. and {Abbott}, T.~M.~C. and {Aguena}, M. and {Annis}, J. and {Bacon}, D. and {Bhargava}, S. and {Brooks}, D. and {Burke}, D.~L. and {Carrasco Kind}, M. and {Carretero}, J. and {Castander}, F.~J. and {Conselice}, C. and {Costanzi}, M. and {da Costa}, L.~N. and {Pereira}, M.~E.~S. and {De Vicente}, J. and {DeRose}, J. and {Desai}, S. and {Eifler}, T.~F. and {Evrard}, A.~E. and {Ferrero}, I. and {Fosalba}, P. and {Frieman}, J. and {Garc{\'\i}a-Bellido}, J. and {Gaztanaga}, E. and {Gerdes}, D.~W. and {Gutierrez}, G. and {Hinton}, S.~R. and {Hollowood}, D.~L. and {Honscheid}, K. and {Huterer}, D. and {James}, D.~J. and {Kent}, S. and {Krause}, E. and {Kuehn}, K. and {Lahav}, O. and {Lima}, M. and {Lin}, H. and {Maia}, M.~A.~G. and {Marshall}, J.~L. and {Melchior}, P. and {Menanteau}, F. and {Miquel}, R. and {Mohr}, J.~J. and {Morgan}, R. and {Muir}, J. and {Ogando}, R.~L.~C. and {Palmese}, A. and {Paz-Chinch{\'o}n}, F. and {Plazas}, A.~A. and {Rodriguez-Monroy}, M. and {Romer}, A.~K. and {Roodman}, A. and {Sanchez}, E. and {Scarpine}, V. and {Serrano}, S. and {Smith}, M. and {Soares-Santos}, M. and {Suchyta}, E. and {Swanson}, M.~E.~C. and {Tarle}, G. and {To}, C. and {Troxel}, M.~A. and {Varga}, T.~N. and {Weller}, J. and {Wilkinson}, R.~D. and {Wilkinson}, R.~D.},
+ title = "{Dark Energy Survey Year 3 Results: Measuring the Survey Transfer Function with Balrog}",
+ journal = {\apjs},
+ keywords = {343, 1464, 351, 1857, Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
+ year = 2022,
+ month = jan,
+ volume = {258},
+ number = {1},
+ eid = {15},
+ pages = {15},
+ doi = {10.3847/1538-4365/ac26c1},
+archivePrefix = {arXiv},
+ eprint = {2012.12825},
+ primaryClass = {astro-ph.CO},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2022ApJS..258...15E},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
@ARTICLE{2002AA_395_1061G,
author = {{Greisen}, E.~W. and {Calabretta}, M.~R.},
title = "{Representations of world coordinates in FITS}",
@@ -283,6 +303,18 @@ archivePrefix = "arXiv",
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
+@ARTICLE{1895RSTA_0010,
+ author = {{Pearson}, K.},
+ title = "{Contributions to the mathematical theory of evolution.—II. Skew variation in homogeneous material}",
+ journal = {Philosophical Transactions of the Royal Society of London},
+ year = 1895,
+ month = jan,
+ volume = 186,
+ pages = {343-414},
+ doi = {10.1098/rsta.1895.0010},
+ url = {https://dx.doi.org/10.1098/rsta.1895.0010},
+}
+
@ARTICLE{1976ApJ_209L_1P,
author = {{Petrosian}, V.},
title = "{Surface brightness and evolution of galaxies}",
@@ -340,13 +372,13 @@ author={{Saerens}, M. and {Latinne}, P. and {Decaestecker}, C.},
journal={IEEE Transactions on Neural Networks},
title={Any reasonable cost function can be used for a posteriori probability approximation},
year={2002},
+month={Sep},
volume={13},
number={5},
pages={1204-1210},
keywords={Bayes methods;decision theory;learning (artificial intelligence);Bayes decision making;a posteriori probability;class membership;cost function;learning machine;loss function;subjective probability theory;Artificial intelligence;Artificial neural networks;Bayesian methods;Computational modeling;Cost function;Decision making;Input variables;Laboratories;Machine learning;Mean square error methods},
doi={10.1109/TNN.2002.1031952},
ISSN={1045-9227},
-month={Sep}
}
@ARTICLE{1987PASP_99_191S,
@@ -542,6 +574,15 @@ publisher = {Cordoba, Argentina: Observatorio Astronomico, 1968},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
+@BOOK{1911AITS,
+ author = {{Yule}, G.~U.},
+ title = "{ An introduction to the theory of statistics}",
+publisher = {C. Griffin and Company, limited},
+ year = 1911,
+ url = {https://archive.org/details/anintroductiont01yulegoog/page/n139/mode/2up},
+}
+
+
@PHDTHESIS{1996PhDT_68B,
author = {{Bertin}, E.},
title = "{Photom\'etrie automatique de galaxies et contraintes sur leur \'evolution r\'ecente}",
diff --git a/doc/theme/images/astromaticO.png b/doc/theme/images/astromaticO.png
new file mode 100644
index 0000000000000000000000000000000000000000..025385fcc87e450925e2d98bafe34e36948d8f28
Binary files /dev/null and b/doc/theme/images/astromaticO.png differ
diff --git a/m4/acx_cfitsio.m4 b/m4/acx_cfitsio.m4
new file mode 100644
index 0000000000000000000000000000000000000000..cc1c0d0b487e54993c0ec17bfb671a184cf97534
--- /dev/null
+++ b/m4/acx_cfitsio.m4
@@ -0,0 +1,115 @@
+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 .
+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)
+ $4
+fi
+
+])dnl ACX_CFITSIO
diff --git a/m4/acx_mkl.m4 b/m4/acx_mkl.m4
index 68c016a97f2a5fad20dac88cce25d72bc8df7118..9ae81e80e750781f7f44fd105724f4a17b4cef81 100644
--- a/m4/acx_mkl.m4
+++ b/m4/acx_mkl.m4
@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
dnl This file part of: AstrOmatic software
dnl
-dnl Copyright: (C) 2003-2016 IAP/CNRS/UPMC
+dnl Copyright: (C) 2003-2022 IAP/CNRS/SorbonneU
dnl
dnl License: GNU General Public License
dnl
@@ -23,7 +23,7 @@ dnl You should have received a copy of the GNU General Public License
dnl along with AstrOmatic software.
dnl If not, see .
dnl
-dnl Last modified: 16/03/2016
+dnl Last modified: 15/09/2022
dnl
dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
@@ -73,11 +73,11 @@ dnl Set architecture flags
dnl ----------------------
dnl check if INTEL compiler is present
-icc -V 2>&1 | grep -i "Intel" > /dev/null 2>&1 && flagicc=yes
+$CC -V 2>&1 | grep -i "Intel" > /dev/null 2>&1 && flagicc=yes
dnl check if INTEL compiler uses x86_64 architecture
-icc -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 && flag64=yes
+$CC -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 && flag64=yes
dnl check if the platform is OSX
-icc -dumpmachine 2>&1 | grep -i "darwin" > /dev/null 2>&1 && flagosx=yes
+$CC -dumpmachine 2>&1 | grep -i "darwin" > /dev/null 2>&1 && flagosx=yes
dnl ----------------------
dnl Exit if INTEL compiler is not found
diff --git a/m4/acx_prog_cc_optim.m4 b/m4/acx_prog_cc_optim.m4
index dff95a109c354e79e3d566199f0bc2af347757f1..3b56a7ce40863bdffc376081e889c5c93480aae7 100644
--- a/m4/acx_prog_cc_optim.m4
+++ b/m4/acx_prog_cc_optim.m4
@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
dnl This file part of: AstrOmatic software
dnl
-dnl Copyright: (C) 2002-2013 Emmanuel Bertin -- IAP/CNRS/UPMC
+dnl Copyright: (C) 2002-2022 Emmanuel Bertin -- IAP/CNRS/SorbonneU
dnl (C) 2002 Ville Lauriki (original version)
dnl
dnl Licenses: GPL (this version)
@@ -25,7 +25,7 @@ dnl You should have received a copy of the GNU General Public License
dnl along with AstrOmatic software.
dnl If not, see .
dnl
-dnl Last modified: 13/03/2013
+dnl Last modified: 07/09/2022
dnl
dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
@@ -60,14 +60,14 @@ EOF
if $CC -V 2>&1 | grep -i "Intel(R) 64" > /dev/null 2>&1 &&
$CC -c -O conftest.c > /dev/null 2>&1 &&
test -f conftest.o; then
- prog_cc_optim_cv_flags="-O3 -axSSSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I -no-prec-div -unroll"
+ prog_cc_optim_cv_flags="-O3 -axSSSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I"
prog_ld_optim_cv_flags=""
dnl INTEL C 32bits compiler
elif $CC -V 2>&1 | grep -i "Intel(R)" > /dev/null 2>&1 &&
$CC -c -O conftest.c > /dev/null 2>&1 &&
test -f conftest.o; then
- prog_cc_optim_cv_flags="-O3 -axSSE2,SSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I -no-prec-div -unroll"
+ prog_cc_optim_cv_flags="-O3 -axSSE2,SSE3,SSE4.1,SSE4.2,AVX,CORE-AVX2,CORE-AVX-I"
prog_ld_optim_cv_flags=""
dnl GCC
diff --git a/m4/acx_pthread.m4 b/m4/acx_pthread.m4
index 4d6003127549197bc4c1c59e1f8bd82910472144..0f8695ff15f8dfd6d9fd3b00dd4080ad8919d03e 100644
--- a/m4/acx_pthread.m4
+++ b/m4/acx_pthread.m4
@@ -7,7 +7,7 @@ dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
dnl This file part of: AstrOmatic software
dnl
-dnl Copyright: (C) 2002-2010 Emmanuel Bertin -- IAP/CNRS/UPMC
+dnl Copyright: (C) 2002-2022 Emmanuel Bertin -- IAP/CNRS/SorbonneU
dnl (C) 2001 Steven G. Johnson (original version)
dnl
dnl Licenses: GPL (this version)
@@ -25,7 +25,7 @@ dnl You should have received a copy of the GNU General Public License
dnl along with AstrOmatic software.
dnl If not, see .
dnl
-dnl Last modified: 09/10/2010
+dnl Last modified: 15/09/2022
dnl
dnl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
dnl
@@ -88,7 +88,7 @@ if test x"$PTHREAD_LIBS$PTHREAD_CFLAGS" != x; then
save_LIBS="$LIBS"
LIBS="$PTHREAD_LIBS $LIBS"
AC_MSG_CHECKING([for pthread_join in LIBS=$PTHREAD_LIBS with CFLAGS=$PTHREAD_CFLAGS])
- AC_TRY_LINK_FUNC(pthread_join, acx_pthread_ok=yes)
+ AC_LINK_IFELSE([AC_LANG_CALL([], pthread_join)], acx_pthread_ok=yes)
AC_MSG_RESULT($acx_pthread_ok)
if test x"$acx_pthread_ok" = xno; then
PTHREAD_LIBS=""
@@ -170,10 +170,10 @@ for flag in $acx_pthread_flags; do
# pthread_cleanup_push because it is one of the few pthread
# functions on Solaris that doesn't have a non-functional libc stub.
# We try pthread_create on general principles.
- AC_TRY_LINK([#include ],
+ AC_LINK_IFELSE([AC_LANG_CALL([#include ],
[pthread_t th; pthread_join(th, 0);
pthread_attr_init(0); pthread_cleanup_push(0, 0);
- pthread_create(0,0,0,0); pthread_cleanup_pop(0); ],
+ pthread_create(0,0,0,0); pthread_cleanup_pop(0); ])],
[acx_pthread_ok=yes])
LIBS="$save_LIBS"
@@ -199,12 +199,12 @@ if test "x$acx_pthread_ok" = xyes; then
# Detect AIX lossage: threads are created detached by default
# and the JOINABLE attribute has a nonstandard name (UNDETACHED).
AC_MSG_CHECKING([for joinable pthread attribute])
- AC_TRY_LINK([#include ],
- [int attr=PTHREAD_CREATE_JOINABLE;],
+ AC_LINK_IFELSE([AC_LANG_CALL([#include ],
+ [int attr=PTHREAD_CREATE_JOINABLE;])],
ok=PTHREAD_CREATE_JOINABLE, ok=unknown)
if test x"$ok" = xunknown; then
- AC_TRY_LINK([#include ],
- [int attr=PTHREAD_CREATE_UNDETACHED;],
+ AC_LINK_IFELSE([AC_LANG_CALL([#include ],
+ [int attr=PTHREAD_CREATE_UNDETACHED;])],
ok=PTHREAD_CREATE_UNDETACHED, ok=unknown)
fi
if test x"$ok" != xPTHREAD_CREATE_JOINABLE; then
diff --git a/sextractor.spec.in b/sextractor.spec.in
index de2b5bd63710e621204139dd62337ebfc7305a53..aee6ced04b936d9f28ae6d6175f49e1a175b737b 100644
--- a/sextractor.spec.in
+++ b/sextractor.spec.in
@@ -7,7 +7,7 @@
#
# This file part of: SExtractor
#
-# Copyright: (C) 2002-2020 IAP/CNRS/SorbonneU
+# Copyright: (C) 2002-2022 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 .
#
-# Last modified: 02/01/2020
+# Last modified: 15/09/2022
#
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -44,6 +44,7 @@ BuildRoot: %{_tmppath}/%{name}-buildroot
BuildRequires: pkgconfig
BuildRequires: fftw-devel >= 3.1
BuildRequires: atlas-devel >= 3.6.0
+BuildRequires: cfitsio-devel >= 3.30
%description
Extract catalogs of sources from astronomical images
diff --git a/src/analyse.c b/src/analyse.c
index f5c6ece9c3f5e70c82b617c42a571ab947b533dd..dcac1ba52418767a948ab42bd73a1af1959df3e7 100644
--- a/src/analyse.c
+++ b/src/analyse.c
@@ -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)
{
@@ -718,10 +717,10 @@ void endobject(picstruct *field, picstruct *dfield, picstruct *wfield,
dgeo_copy(dgeofield, outobj2.vignet_dgeox , outobj2.vignet_dgeoy,
prefs.vignet_dgeoxsize[0],prefs.vignet_dgeoxsize[1], ix,iy);
else {
- if (FLAG(obj2.vignet_dgeox))
+ if (FLAG(obj2.vignet_dgeox))
dgeo_copy(dgeofield, outobj2.vignet_dgeox, NULL,
prefs.vignet_dgeoxsize[0],prefs.vignet_dgeoxsize[1], ix,iy);
- if (FLAG(obj2.vignet_dgeoy))
+ if (FLAG(obj2.vignet_dgeoy))
dgeo_copy(dgeofield, NULL, outobj2.vignet_dgeoy,
prefs.vignet_dgeoysize[0],prefs.vignet_dgeoysize[1], ix,iy);
}
diff --git a/src/back.c b/src/back.c
index a77118bf70906c54c393c9eb59cdf434dbceeead..355fa01c46d5d4806fe459343b2e4d50c9d62b52 100644
--- a/src/back.c
+++ b/src/back.c
@@ -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 .
*
-* 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)");
@@ -625,7 +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' */
@@ -641,6 +689,8 @@ float backguess(backstruct *bkg, float *mean, float *sigma)
sig = 10.0*nlevelsm1;
sig1 = 1.0;
+ medfac = prefs.back_pearson;
+ meafac = prefs.back_pearson - 1.0;
mea = med = bkg->mean;
for (n=100; n-- && (sig>=0.1) && (fabs(sig/sig1-1.0)>EPS);)
{
@@ -677,7 +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;
diff --git a/src/catout.c b/src/catout.c
index 5e1ff7ad094f333f6d05750f3a4b2ffab22b3d15..bd8569fe6b47f2f527964b9ca9ba1eaa61367d61 100644
--- a/src/catout.c
+++ b/src/catout.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2020 IAP/CNRS/SorbonneU
+* Copyright: (C) 1993-2023 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 .
*
-* Last modified: 15/07/2020
+* Last modified: 26/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -1059,7 +1059,7 @@ void reendcat()
{
keystruct *key;
tabstruct *tab;
- OFF_T pos;
+ OFF_T2 pos;
char *head;
switch(prefs.cat_type)
@@ -1086,6 +1086,7 @@ void reendcat()
QFTELL(fitscat->file, pos, fitscat->filename);
QFSEEK(fitscat->file, tab->headpos, SEEK_SET, fitscat->filename);
save_tab(fitscat, tab);
+ remove_tab(fitscat, "LDAC_IMHEAD", 0);
QFSEEK(fitscat->file, pos, SEEK_SET, fitscat->filename);
break;
@@ -1127,4 +1128,3 @@ void zerocat(void)
}
-
diff --git a/src/check.c b/src/check.c
index 933d625e28dd7ef041ed2c1c8b064628eef1d1c3..397e5be1586047eca9cac69833498428e0040865 100644
--- a/src/check.c
+++ b/src/check.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2013 Emmanuel Bertin -- IAP/CNRS/UPMC
+* Copyright: (C) 1993-2023 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 .
*
-* Last modified: 23/09/2013
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -406,6 +406,7 @@ void reinitcheck(picstruct *field, checkstruct *check)
remove_tabs(cat);
copy_tab_fromptr(field->tab, cat, 0);
tab = cat->tab;
+ decomp_head(tab);
tab->cat = cat;
if (check->next<=1)
prim_head(tab);
diff --git a/src/define.h b/src/define.h
index 0123b13dacd523c82ecb4ab4d20420a9aa47cf98..22653bbe2ebd94a7978a22f050e7ed40b660b00a 100644
--- a/src/define.h
+++ b/src/define.h
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2015 Emmanuel Bertin -- IAP/CNRS/UPMC
+* Copyright: (C) 1993-2022 Emmanuel Bertin -- 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 .
*
-* Last modified: 11/03/2015
+* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -167,7 +167,7 @@
#define QCALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)calloc((size_t)(nel),sizeof(typ)))) \
{ \
- sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
@@ -177,7 +177,7 @@
#define QMALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)malloc((size_t)(nel)*sizeof(typ)))) \
{ \
- sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
@@ -187,7 +187,7 @@
#define QMALLOC16(ptr, typ, nel) \
{if (posix_memalign((void **)&ptr, 16, (size_t)(nel)*sizeof(typ))) \
{ \
- sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
@@ -197,7 +197,7 @@
#define QREALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)realloc(ptr, (size_t)(nel)*sizeof(typ))))\
{ \
- sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
@@ -208,7 +208,7 @@
{if (ptrin) \
{if (!(ptrout = (typ *)malloc((size_t)(nel)*sizeof(typ)))) \
{ \
- sprintf(gstr, #ptrout " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptrout " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE,"Could not allocate memory for ",gstr);\
diff --git a/src/fft.h b/src/fft.h
index a894528e1a684e89e6f922359b7836a4566de5c9..1e33af6f4ee6d2b58895b80a82516a0c3f583283 100644
--- a/src/fft.h
+++ b/src/fft.h
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 2007-2017 IAP/CNRS/UPMC
+* Copyright: (C) 2007-2022 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 .
*
-* Last modified: 19/06/2017
+* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -40,7 +40,7 @@
#define QFFTWF_MALLOC(ptr, typ, nel) \
{if (!(ptr = (typ *)fftwf_malloc((size_t)(nel)*sizeof(typ)))) \
{ \
- sprintf(gstr, #ptr " (" #nel "=%lld elements) " \
+ sprintf(gstr, #ptr " (" #nel "=%zd elements) " \
"at line %d in module " __FILE__ " !", \
(size_t)(nel)*sizeof(typ), __LINE__); \
error(EXIT_FAILURE, "Could not allocate memory for ", gstr);\
diff --git a/src/field.c b/src/field.c
index e396853475c1b8e596b1155a0537e408ab570d9b..743adfdb2c5762dbff9b66ae96a2c5678304f7f3 100644
--- a/src/field.c
+++ b/src/field.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2012 Emmanuel Bertin -- IAP/CNRS/UPMC
+* Copyright: (C) 1993-2023 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 .
*
-* Last modified: 12/07/2012
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -70,21 +70,41 @@ picstruct *newfield(char *filename, int flags, int ext)
field->cat = cat;
nok = 0;
tab = cat->tab;
+#ifdef HAVE_CFITSIO
+ if ((tab->isTileCompressed) ||
+ (tab->naxis >= 2
+ && strncmp(tab->xtension, "BINTABLE", 8)
+ && strncmp(tab->xtension, "ASCTABLE", 8)))
+#else
+ if (tab->isTileCompressed)
+ warning(BANNER " has been compiled without CFITSIO support: "
+ "compressed image skipped in ", filename);
if (tab->naxis >= 2
&& strncmp(tab->xtension, "BINTABLE", 8)
&& strncmp(tab->xtension, "ASCTABLE", 8))
+#endif
nok++;
ext2 = ext;
for (ntab=cat->ntab; ext2-- && ntab--;)
{
tab=tab->nexttab;
+#ifdef HAVE_CFITSIO
+ if ((tab->isTileCompressed) ||
+ (tab->naxis >= 2
+ && strncmp(tab->xtension, "BINTABLE", 8)
+ && strncmp(tab->xtension, "ASCTABLE", 8)))
+#else
+ if (tab->isTileCompressed)
+ warning(BANNER " has been compiled without CFITSIO support: "
+ "compressed image skipped in ", filename);
if (tab->naxis >= 2
- && strncmp(tab->xtension, "BINTABLE", 8)
- && strncmp(tab->xtension, "ASCTABLE", 8))
+ && strncmp(tab->xtension, "BINTABLE", 8)
+ && strncmp(tab->xtension, "ASCTABLE", 8))
+#endif
nok++;
}
if (!nok)
- error(EXIT_FAILURE, "Not a valid FITS image in ",filename);
+ error(EXIT_FAILURE, "Not a valid FITS image in ", filename);
field->tab = tab;
if (ntab<0)
diff --git a/src/fits/fitsbody.c b/src/fits/fitsbody.c
index c4229f6cf1bbe5883daf8f5a635a4fc65d97cbc4..90bcd276fe8163a1a25f1ffda9349d8f9a314598 100644
--- a/src/fits/fitsbody.c
+++ b/src/fits/fitsbody.c
@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
-* Copyright: (C) 1995-2010 IAP/CNRS/SorbonneU
+* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 11/02/2020
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -43,6 +43,10 @@
#include "fitscat_defs.h"
#include "fitscat.h"
+#ifdef HAVE_CFITSIO
+#include CFITSIO_H
+#endif
+
size_t body_maxram = BODY_DEFRAM,
body_maxvram = BODY_DEFVRAM,
body_ramleft, body_vramleft, body_ramflag;
@@ -60,7 +64,7 @@ INPUT Table (tab) structure.
OUTPUT Pointer to the mapped data if OK, or NULL otherwise.
NOTES The file pointer must be positioned at the beginning of the data.
AUTHOR E. Bertin (IAP)
-VERSION 05/05/2001
+VERSION 02/10/2017
***/
PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
{
@@ -85,7 +89,11 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
tab->extname);
/* Decide if the data will go in physical memory or on swap-space */
+#ifdef HAVE_CFITSIO
+ npix = tab->naxisn[0] * tab->naxisn[1];
+#else
npix = tab->tabsize/tab->bytepix;
+#endif
size = npix*sizeof(PIXTYPE);
if (size < body_ramleft)
{
@@ -93,6 +101,9 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
if ((tab->bodybuf = malloc(size)))
{
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
+#ifdef HAVE_CFITSIO
+ tab->currentElement = 1;
+#endif
read_body(tab, (PIXTYPE *)tab->bodybuf, npix);
/*---- Apply pixel processing */
if (func)
@@ -120,6 +131,9 @@ PIXTYPE *alloc_body(tabstruct *tab, void (*func)(PIXTYPE *ptr, int npix))
if (!spoonful)
spoonful = DATA_BUFSIZE;
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
+#ifdef HAVE_CFITSIO
+ tab->currentElement = 1;
+#endif
read_body(tab, buffer, spoonful/sizeof(PIXTYPE));
/*-- Apply pixel processing */
if (func)
@@ -159,7 +173,7 @@ INPUT Table (tab) structure.
OUTPUT Pointer to the mapped data if OK, or NULL otherwise.
NOTES The file pointer must be positioned at the beginning of the data.
AUTHOR E. Bertin (IAP)
-VERSION 30/01/2012
+VERSION 02/10/2017
***/
FLAGTYPE *alloc_ibody(tabstruct *tab,
void (*func)(FLAGTYPE *ptr, int npix))
@@ -193,6 +207,9 @@ FLAGTYPE *alloc_ibody(tabstruct *tab,
if ((tab->bodybuf = malloc(size)))
{
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
+#ifdef HAVE_CFITSIO
+ tab->currentElement = 1;
+#endif
read_ibody(tab, (FLAGTYPE *)tab->bodybuf, npix);
/*---- Apply pixel processing */
if (func)
@@ -220,6 +237,9 @@ FLAGTYPE *alloc_ibody(tabstruct *tab,
if (!spoonful)
spoonful = DATA_BUFSIZE;
QFSEEK(tab->cat->file, tab->bodypos, SEEK_SET, tab->cat->filename);
+#ifdef HAVE_CFITSIO
+ tab->currentElement = 1;
+#endif
read_ibody(tab, buffer, spoonful/sizeof(FLAGTYPE));
/*-- Apply pixel processing */
if (func)
@@ -294,6 +314,77 @@ void free_body(tabstruct *tab)
return;
}
+#ifdef HAVE_CFITSIO
+/******* readTileCompressed ***************************************************
+ *
+ * Function to read a chunk of a tile-compressed FITS image
+ *
+ ***/
+void readTileCompressed(tabstruct *tab, size_t spoonful, void *bufdata0) {
+
+ int status, hdutype;
+
+ // first of all, move to correct HDU
+ status = 0;
+ fits_movabs_hdu(tab->infptr, tab->hdunum, &hdutype, &status);
+ if (status != 0) {
+ printf("Error moving to HDU %d\n", tab->hdunum);
+ fits_report_error(stderr, status);
+ }
+
+ // pixels count from 1
+ if (!tab->currentElement)
+ tab->currentElement = 1;
+
+ // now read section of image
+ int datatype;
+ switch(tab->bitpix){
+ case BYTE_IMG:
+ datatype = TBYTE;
+ break;
+ case SHORT_IMG:
+ datatype = TSHORT;
+ break;
+ case LONG_IMG:
+ datatype = TLONG;
+ break;
+ case FLOAT_IMG:
+ datatype = TFLOAT;
+ break;
+ case DOUBLE_IMG:
+ datatype = TDOUBLE;
+ break;
+ default:
+ datatype = TFLOAT;
+ break;
+ }
+
+ int anynul;
+ double bscale = 1.0, bzero = 0.0, nulval = 0.;
+
+ // turn off any scaling so that we copy raw pixel values
+ status = 0;
+ fits_set_bscale(tab->infptr, bscale, bzero, &status);
+
+ // now read the image
+ status = 0;
+ fits_read_img(tab->infptr, datatype, tab->currentElement, spoonful, &nulval,
+ bufdata0, &anynul, &status);
+
+ // report reading error
+ if (status) {
+ printf("CFITSIO ERROR reading start=%d end=%d absolute end=%d\n",
+ tab->currentElement,
+ (tab->currentElement + spoonful),
+ (tab->naxisn[0]*tab->naxisn[1]));
+ fits_report_error(stderr, status);
+ }
+
+ // update file 'pointer'
+ tab->currentElement += spoonful;
+}
+
+#endif // HAVE_CFITSIO
/******* read_body ************************************************************
PROTO read_body(tabstruct *tab, PIXTYPE *ptr, long size)
@@ -303,8 +394,8 @@ INPUT A pointer to the tab structure,
the number of elements to be read.
OUTPUT -.
NOTES .
-AUTHOR E. Bertin (IAP)
-VERSION 11/02/2020
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
***/
void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
{
@@ -323,15 +414,15 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
int curval, dval, blankflag, bswapflag, ival, iblank;
size_t i, bowl, spoonful, npix;
- PIXTYPE bs,bz;
-
+ double bs,bz;
/* a NULL cat structure indicates that no data can be read */
if (!(cat = tab->cat))
return;
- bs = (PIXTYPE)tab->bscale;
- bz = (PIXTYPE)tab->bzero;
+ bs = tab->bscale;
+ bz = tab->bzero;
+
blankflag = tab->blankflag;
bswapflag = *((char *)&ashort); // Byte-swapping flag
@@ -346,7 +437,15 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
if (spoonful>size)
spoonful = size;
bufdata = (char *)bufdata0;
+
+#ifdef HAVE_CFITSIO
+ if (tab->isTileCompressed && tab->infptr)
+ readTileCompressed(tab, spoonful, (void *)bufdata0);
+ else
+ QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
+#else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
+#endif // HAVE_CFITSIO
switch(tab->bitpix)
{
case BP_BYTE:
@@ -383,7 +482,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
case BP_SHORT:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 2, spoonful);
if (blankflag)
{
@@ -418,7 +521,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
case BP_LONG:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 4, spoonful);
if (blankflag)
{
@@ -454,7 +561,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
#ifdef HAVE_LONG_LONG_INT
case BP_LONGLONG:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 8, spoonful);
if (blankflag)
{
@@ -489,7 +600,11 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
break;
#endif
case BP_FLOAT:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 4, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(float))
@@ -499,7 +614,12 @@ void read_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
case BP_DOUBLE:
if (bswapflag)
{
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed)
+ swapbytes(bufdata, 8, spoonful);
+#else
swapbytes(bufdata, 8, spoonful);
+#endif
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(double))
*(ptr++) = ((0x7ff00000 & *(unsigned int *)(bufdata+4))
@@ -632,7 +752,7 @@ INPUT A pointer to the tab structure,
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
-VERSION 11/02/2020
+VERSION 26/08/2020
***/
void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
{
@@ -660,7 +780,15 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
if (spoonful>size)
spoonful = size;
bufdata = (char *)bufdata0;
+
+#ifdef HAVE_CFITSIO
+ if (tab->isTileCompressed)
+ readTileCompressed(tab, spoonful, (void *)bufdata0);
+ else
+ QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
+#else
QFREAD(bufdata, spoonful*tab->bytepix, cat->file, cat->filename);
+#endif
switch(tab->bitpix)
{
case BP_BYTE:
@@ -670,7 +798,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
break;
case BP_SHORT:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 2, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(unsigned short))
@@ -678,7 +810,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
break;
case BP_LONG:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 4, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(unsigned int))
@@ -687,7 +823,11 @@ void read_ibody(tabstruct *tab, FLAGTYPE *ptr, size_t size)
#ifdef HAVE_LONG_LONG_INT
case BP_LONGLONG:
+#ifdef HAVE_CFITSIO
+ if (!tab->isTileCompressed && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(bufdata, 8, spoonful);
#pragma ivdep
for (i=spoonful; i--; bufdata += sizeof(ULONGLONG))
@@ -815,7 +955,7 @@ INPUT A pointer to the tab structure,
OUTPUT -.
NOTES .
AUTHOR E. Bertin (IAP)
-VERSION 11/02/2020
+VERSION 26/08/2020
***/
void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
{
@@ -931,7 +1071,12 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
#pragma ivdep
for (i=spoonful; i--;)
*(bufdata++) = (*(ptr++)-bz)/bs;
+
+#ifdef HAVE_CFITSIO
+ if (!tab->infptr && bswapflag)
+#else
if (bswapflag)
+#endif
swapbytes(cbufdata0, 4, spoonful);
}
break;
@@ -952,7 +1097,61 @@ void write_body(tabstruct *tab, PIXTYPE *ptr, size_t size)
"read_body()");
break;
}
+
+#ifdef HAVE_CFITSIO
+ // if cfitsio output file has been set up, then proceed to write
+ if (tab->infptr) {
+ // now read section of image
+ int datatype;
+ switch(tab->bitpix) {
+ case BYTE_IMG:
+ datatype = TBYTE;
+ break;
+ case SHORT_IMG:
+ datatype = TSHORT;
+ break;
+ case LONG_IMG:
+ datatype = TLONG;
+ break;
+ case FLOAT_IMG:
+ datatype = TFLOAT;
+ break;
+ case DOUBLE_IMG:
+ datatype = TDOUBLE;
+ break;
+ default:
+ datatype = TFLOAT;
+ break;
+ }
+
+ // turn off any scaling so that we copy the raw pixel values
+ double *array,
+ bscale = 1.0,
+ bzero = 0.0,
+ nulval = 0.0;
+
+ int status = 0;
+
+ fits_set_bscale(tab->infptr, bscale, bzero, &status);
+ status = 0;
+ fits_write_img(tab->infptr, datatype, tab->currentElement, spoonful,
+ cbufdata0, &status);
+
+ if (status) {
+
+ printf("CFITSIO ERROR writing start=%d end=%d absolute end=%d\n",
+ tab->currentElement, (tab->currentElement + spoonful),
+ (tab->naxisn[0]*tab->naxisn[1]));
+ fits_report_error(stderr, status);
+ }
+
+ tab->currentElement = tab->currentElement + spoonful;
+ } else
+ // otherwise, continue with usual AstrOmatic fits writing routine
+ QFWRITE(cbufdata0, spoonful*tab->bytepix, cat->file, cat->filename);
+#else
QFWRITE(cbufdata0, spoonful*tab->bytepix, cat->file, cat->filename);
+#endif // HAVE_CFITSIO
}
break;
diff --git a/src/fits/fitscat.c b/src/fits/fitscat.c
index 4e8bc05fec6e486939a11b49914ec0a43d72dc57..efe9a0cac976f1d23e0a3e77d972c1bb2d9e82c9 100644
--- a/src/fits/fitscat.c
+++ b/src/fits/fitscat.c
@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
-* Copyright: (C) 1995-2020 IAP/CNRS/SorbonneU
+* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 15/07/2020
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -42,6 +42,8 @@
#include "fitscat_defs.h"
#include "fitscat.h"
+extern float *fits_rand_value;
+
char fits_str[MAXCHAR];
/****** about_cat **************************************************************
@@ -167,6 +169,37 @@ int close_cat(catstruct *cat)
return RETURN_OK;
}
+#ifdef HAVE_CFITSIO
+/****** close_cfitsio **********************************************************
+PROTO int close_cfitsio(fitsfile **infptr)
+PURPOSE Close a file previously opened by cfitsio
+INPUT fitsfile structure.
+OUTPUT RETURN_OK if everything went as expected (exit in error otherwise).
+NOTES the fitsfile pointer is set to NULL;
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
+***/
+int close_cfitsio(catstruct *cat) {
+
+ if ((cat) && (cat->infptr)) {
+ int status = 0; fits_close_file(cat->infptr, &status);
+
+ if (status != 0) {
+ fits_report_error(stderr, status);
+ error(EXIT_FAILURE, "Could not close FITS file with cfitsio: ",
+ cat->filename);
+ } else {
+ // Successfully closed FITS file with cfitsio
+ cat->infptr == NULL;
+ // Free random seed in CFITSIO.
+ QFREE(fits_rand_value);
+ }
+ } else
+ return RETURN_ERROR;
+ return RETURN_OK;
+}
+#endif // HAVE_CFITSIO
+
/****** free_cat ***************************************************************
PROTO void free_cat(catstruct **cat, int ncat)
@@ -175,8 +208,8 @@ INPUT Pointer to a catalog structure,
Number of catalogs.
OUTPUT -.
NOTES Unallocated pointers should have been put to NULL.
-AUTHOR E. Bertin (IAP & Leiden observatory)
-VERSION 05/12/2009
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
***/
void free_cat(catstruct **cat, int ncat)
@@ -191,6 +224,10 @@ void free_cat(catstruct **cat, int ncat)
if ((*thecat)->file)
close_cat(*thecat);
remove_tabs(*thecat);
+#ifdef HAVE_CFITSIO
+ // Free resources allocated for CFITSIO
+ close_cfitsio(*thecat);
+#endif
free(*(thecat++));
}
@@ -311,8 +348,8 @@ PURPOSE Explores the whole FITS file
INPUT catalog structure.
OUTPUT RETURN_OK if at least one table was found, RETURN_ERROR otherwise.
NOTES Memory space for the array of fits structures is reallocated.
-AUTHOR E. Bertin (IAP & Leiden observatory)
-VERSION 14/12/2002
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
***/
int map_cat(catstruct *cat)
@@ -325,14 +362,38 @@ int map_cat(catstruct *cat)
QCALLOC(tab, tabstruct, 1);
tab->cat = cat;
QFTELL(cat->file, tab->headpos, cat->filename);
+
+#ifdef HAVE_CFITSIO
+ fitsfile *infptr;
+ int status, hdutype, hdunum = 1;
+#endif // HAVE_CFITSIO
+
for (ntab=0; !get_head(tab); ntab++)
{
readbasic_head(tab);
readbintabparam_head(tab);
QFTELL(cat->file, tab->bodypos, cat->filename);
tab->nseg = tab->seg = 1;
+
+#ifdef HAVE_CFITSIO
+ if (tab->isTileCompressed) {
+ // Trigger CFITSIO file opening
+ status = 0;
+ if (!cat->infptr) {
+ fits_open_file(&cat->infptr, cat->filename, READONLY, &status);
+ if (status != 0) {
+ fits_report_error(stderr, status);
+ error(EXIT_FAILURE,
+ "Could not open FITS file with cfitsio: %s\n", cat->filename);
+ }
+ }
+ tab->infptr = cat->infptr;
+ }
+ tab->hdunum = hdunum++;
+#endif // HAVE_CFITSIO
if (tab->tabsize)
QFSEEK(cat->file, PADTOTAL(tab->tabsize), SEEK_CUR, cat->filename);
+
if (prevtab)
{
tab->prevtab = prevtab;
diff --git a/src/fits/fitscat.h b/src/fits/fitscat.h
index 5e35d2e08ace6359a8a0c1867f3e1c8e5bdf29d1..63bb1c7f0a6db8367f6a94e7bfad8d85365cd940 100644
--- a/src/fits/fitscat.h
+++ b/src/fits/fitscat.h
@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
-* Copyright: (C) 1995-2020 IAP/CNRS/SorbonneU
+* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 11/02/2020
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -36,6 +36,10 @@
#include
#endif
+#ifdef HAVE_CFITSIO
+#include CFITSIO_H
+#endif
+
#define MAXCHARS 256 /* max. number of characters */
#define WARNING_NMAX 1000 /* max. number of recorded warnings */
@@ -107,10 +111,11 @@ typedef long long SLONGLONG;
typedef union {int l[2];} SLONGLONG;
#endif
-#if defined(_FILE_OFFSET_BITS) && !defined(OFF_T)
-#define OFF_T off_t
+// CFITSIO changed OFF_T to OFF_T2 due to clash with cfitsio lib
+#if defined(_FILE_OFFSET_BITS) && !defined(OFF_T2)
+#define OFF_T2 off_t
#else
-#define OFF_T long
+#define OFF_T2 long
#endif
/*------------------------------- constants ---------------------------------*/
@@ -150,6 +155,9 @@ typedef struct structcat
struct structtab *tab; /* pointer to the first table */
int ntab; /* number of tables included */
access_type_t access_type; /* READ_ONLY or WRITE_ONLY */
+#ifdef HAVE_CFITSIO
+ fitsfile *infptr; /* a cfitsio pointer to the file */
+#endif
} catstruct;
/*-------------------------------- table ----------------------------------*/
@@ -180,8 +188,8 @@ typedef struct structtab
char *headbuf; /* buffer containing the header */
int headnblock; /* number of FITS blocks */
char *bodybuf; /* buffer containing the body */
- OFF_T bodypos; /* position of the body in the file */
- OFF_T headpos; /* position of the head in the file */
+ OFF_T2 bodypos; /* position of the body in the file */
+ OFF_T2 headpos; /* position of the head in the file */
struct structcat *cat; /* (original) parent catalog */
struct structtab *prevtab, *nexttab; /* previous and next tab in chain */
int seg; /* segment position */
@@ -190,7 +198,13 @@ typedef struct structtab
int nkey; /* number of keys */
int swapflag; /* mapped to a swap file ? */
char swapname[MAXCHARS]; /* name of the swapfile */
- unsigned int bodysum; /* Checksum of the FITS body */
+ unsigned int bodysum; /* Checksum of the FITS body */
+ int isTileCompressed; /* is this a tile compressed image? */
+#ifdef HAVE_CFITSIO
+ fitsfile *infptr; /* a cfitsio pointer to the file */
+ int hdunum; /* FITS HDU number for this 'table' */
+ long currentElement; /* tracks the current image pixel */
+#endif
} tabstruct;
@@ -218,8 +232,8 @@ extern void add_cleanupfilename(char *filename),
encode_checksum(unsigned int sum, char *str),
end_readobj(tabstruct *keytab, tabstruct *tab, char *buf),
end_writeobj(catstruct *cat, tabstruct *tab, char *buf),
- error(int, char *, char *),
- error_installfunc(void (*func)(char *msg1, char *msg2)),
+ error(int code, const char *msg1, const char *msg2),
+ error_installfunc(void (*func)(const char *msg1, const char *msg2)),
fixexponent(char *s),
free_body(tabstruct *tab),
free_cat(catstruct **cat, int ncat),
@@ -271,6 +285,9 @@ extern int about_cat(catstruct *cat, FILE *stream),
add_tab(tabstruct *tab, catstruct *cat, int pos),
blank_keys(tabstruct *tab),
close_cat(catstruct *cat),
+#ifdef HAVE_CFITSIO
+ close_cfitsio(catstruct *cat),
+#endif
copy_key(tabstruct *tabin, char *keyname, tabstruct *tabout,
int pos),
copy_tab(catstruct *catin, char *tabname, int seg,
@@ -315,6 +332,7 @@ extern int about_cat(catstruct *cat, FILE *stream),
tformof(char *str, t_type ttype, int n),
tsizeof(char *str),
update_head(tabstruct *tab),
+ decomp_head(tabstruct *tab),
update_tab(tabstruct *tab),
verify_checksum(tabstruct *tab),
write_obj(tabstruct *tab, char *buf),
@@ -328,8 +346,4 @@ extern FLAGTYPE *alloc_ibody(tabstruct *tab,
extern t_type ttypeof(char *str);
-extern void error(int, char *, char *),
- swapbytes(void *ptr, int nb, int n),
- warning(char *msg1, char *msg2);
-
#endif
diff --git a/src/fits/fitshead.c b/src/fits/fitshead.c
index 1821b92da5b33fe5b23933746f82d9ffc835280a..5232e685cf574e8216cb792513ca91587e4b02b1 100644
--- a/src/fits/fitshead.c
+++ b/src/fits/fitshead.c
@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
-* Copyright: (C) 1995-2022 IAP/CNRS/SorbonneU
+* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 11/03/2022
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -100,64 +100,92 @@ PURPOSE Read the current FITS header basic keywords.
INPUT pointer to catstruct.
OUTPUT -.
NOTES -.
-AUTHOR E. Bertin (IAP)
-VERSION 03/06/2012
+AUTHOR E. Bertin (CFHT/IAP/SorbonneU)
+VERSION 25/02/2023
***/
void readbasic_head(tabstruct *tab)
{
char str[88];
char key[12], name[16],
- *filename;
- int i;
+ *bitpix_key, *naxis_key, *filename;
+ int i, bitpix, bytepix, naxis, naxisn;
KINGSIZE_T tabsize;
filename = (tab->cat? tab->cat->filename : strcpy(name, "internal header"));
- if (fitsread(tab->headbuf, "BITPIX ", &tab->bitpix, H_INT, T_LONG)
- ==RETURN_ERROR)
- error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
+ tab->isTileCompressed = (fitsread(tab->headbuf, "ZIMAGE ",
+ str, H_STRING, T_STRING) == RETURN_OK)? 1 : 0;
- tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
+ if (fitsread(tab->headbuf, tab->isTileCompressed ? "ZBITPIX " : "BITPIX ",
+ &tab->bitpix, H_INT, T_LONG) == RETURN_ERROR)
+ error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
- if (fitsread(tab->headbuf, "NAXIS ", &tab->naxis, H_INT, T_LONG)
- ==RETURN_ERROR)
+ if (fitsread(tab->headbuf, tab->isTileCompressed ? "ZNAXIS " : "NAXIS ",
+ &tab->naxis, H_INT, T_LONG) == RETURN_ERROR)
error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
- tabsize = 0;
- if (tab->naxis>0)
- {
+ tab->bytepix = tab->bitpix>0?(tab->bitpix/8):(-tab->bitpix/8);
+ if (tab->naxis>0) {
QFREE(tab->naxisn);
QMALLOC(tab->naxisn, int, tab->naxis);
/*--get the size of the array*/
- tabsize = 1;
- for (i=0; inaxis && i<999; i++)
- {
- sprintf(key,"NAXIS%-3d", i+1);
+ for (i=0; inaxis && i<999; i++) {
+ sprintf(key, tab->isTileCompressed? "ZNAXIS%-2d" : "NAXIS%-3d", i+1);
if (fitsread(tab->headbuf, key, &tab->naxisn[i], H_INT, T_LONG)
==RETURN_ERROR)
- error(EXIT_FAILURE, "*Error*: incoherent FITS header in ", filename);
- tabsize *= tab->naxisn[i];
- }
+ error(EXIT_FAILURE, "*Error*: inconsistent FITS header in ", filename);
}
+ }
-/*random groups parameters (optional)*/
- tab->pcount = 0;
- fitsread(tab->headbuf, "PCOUNT ", &tab->pcount, H_INT, T_LONG);
- tab->gcount = 1;
- fitsread(tab->headbuf, "GCOUNT ", &tab->gcount, H_INT, T_LONG);
-
-/*number of fields (only for tables)*/
- tab->tfields = 0;
- fitsread(tab->headbuf, "TFIELDS ", &tab->tfields, H_INT, T_LONG);
-
-/*in case of a non-primary header*/
+/* In case of a non-primary header*/
tab->xtension[0] = (char)'\0';
fitsread(tab->headbuf, "XTENSION", tab->xtension, H_STRING, T_STRING);
tab->extname[0] = (char)'\0';
fitsread(tab->headbuf, "EXTNAME ", tab->extname, H_STRING, T_STRING);
- tab->tabsize = tab->bytepix*tab->gcount*((size_t)tab->pcount+tabsize);
+/* Number of fields (only for tables)*/
+ tab->tfields = 0;
+ fitsread(tab->headbuf, "TFIELDS ", &tab->tfields, H_INT, T_LONG);
+
+/* Random groups parameters (optional)*/
+ tab->gcount = 1;
+ fitsread(tab->headbuf, "GCOUNT ", &tab->gcount, H_INT, T_LONG);
+ tab->pcount = 0;
+ fitsread(tab->headbuf, "PCOUNT ", &tab->pcount, H_INT, T_LONG);
+
+/* Compute extension body size in bytes */
+ if (tab->isTileCompressed) {
+ if (fitsread(tab->headbuf, "BITPIX ",
+ &bitpix, H_INT, T_LONG) == RETURN_ERROR)
+ error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
+ bytepix = bitpix>0?(bitpix/8):(-bitpix/8);
+
+ if (fitsread(tab->headbuf, "NAXIS ", &naxis, H_INT, T_LONG)
+ ==RETURN_ERROR)
+ error(EXIT_FAILURE, "*Error*: Corrupted FITS header in ", filename);
+ if ((naxis)) {
+ tabsize = 1;
+ for (i=0; iheadbuf, key, &naxisn, H_INT, T_LONG)
+ ==RETURN_ERROR)
+ error(EXIT_FAILURE, "*Error*: inconsistent FITS header in ", filename);
+ tabsize *= naxisn;
+ }
+ } else
+ tabsize = 0;
+ } else {
+ bytepix = tab->bytepix;
+ if ((tab->naxis)) {
+ tabsize = 1;
+ for (i=0; inaxis && i<999; i++)
+ tabsize *= tab->naxisn[i];
+ } else
+ tabsize = 0;
+ }
+ tab->tabsize = bytepix*tab->gcount*((size_t)tab->pcount+tabsize);
/* Scaling parameters for basic FITS integer arrays */
tab->bscale = 1.0;
@@ -284,7 +312,12 @@ int readbintabparam_head(tabstruct *tab)
key->htype = H_STRING;
break;
default:
+#ifdef HAVE_CFITSIO
+ // CFITSIO TODO dodgy
+ key->ttype = T_FLOAT;
+#else
error(EXIT_FAILURE, "*Error*: Unknown TFORM in ", cat->filename);
+#endif
}
/*--handle the special case of multimensional arrays*/
@@ -893,3 +926,49 @@ char *printftotdisp(char *cprintf, char *str)
return str;
}
+
+/****** decomp_head ***********************************************************
+PROTO int decomp_head(tabstruct *tab)
+PURPOSE Update a FITS header so that it now matches uncompressed data format.
+INPUT Table structure.
+OUTPUT RETURN_OK if tab is a compressed binary table,
+ or RETURN_ERROR otherwise.
+NOTES The headbuf pointer in the tabstruct might be reallocated.
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
+ ***/
+int decomp_head(tabstruct *tab) {
+
+#ifdef HAVE_CFITSIO
+/* Update XTENSION, the extension type */
+ if (tab->isTileCompressed && *tab->xtension) {
+ strcpy(tab->xtension, "IMAGE");
+ addkeywordto_head(tab, "XTENSION", "EXTENSION TYPE");
+ fitswrite(tab->headbuf, "XTENSION", tab->xtension, H_STRING, T_STRING);
+ addkeywordto_head(tab, "PCOUNT ", "required keyword; must = 0");
+ addkeywordto_head(tab, "GCOUNT ", "required keyword; must = 1");
+ tab->pcount = 0;
+ tab->gcount = 1;
+ fitswrite(tab->headbuf,"PCOUNT ", &tab->pcount, H_INT, T_LONG);
+ fitswrite(tab->headbuf,"GCOUNT ", &tab->gcount, H_INT, T_LONG);
+ tab->isTileCompressed = 0;
+
+/*-- Remove all compression-related keywords */
+ removekeywordfrom_head(tab, "TFIELDS?");
+ removekeywordfrom_head(tab, "TTYPE???");
+ removekeywordfrom_head(tab, "TFORM???");
+ removekeywordfrom_head(tab, "ZIMAGE??");
+ removekeywordfrom_head(tab, "ZBITPIX?");
+ removekeywordfrom_head(tab, "ZNAXIS??");
+ removekeywordfrom_head(tab, "ZTILE???");
+ removekeywordfrom_head(tab, "ZCMPTYPE");
+ removekeywordfrom_head(tab, "ZNAME???");
+ removekeywordfrom_head(tab, "ZVAL????");
+ update_head(tab);
+ return RETURN_OK;
+ } else
+#endif
+ return RETURN_ERROR;
+}
+
+
diff --git a/src/fits/fitskey.c b/src/fits/fitskey.c
index 8ca41c2b5896c7d57fb58db10a63e4b922b9a043..72fcbabb929b33c8b3f768c0b09a5de2a180cbc2 100644
--- a/src/fits/fitskey.c
+++ b/src/fits/fitskey.c
@@ -991,7 +991,7 @@ void show_keys(tabstruct *tab, char **keynames, keystruct **keys, int nkeys,
if (kflag)
free(keys);
if (o_type == SHOW_SKYCAT)
- fprintf(stream, skycattail, 1.0);
+ fprintf(stream, "%s", skycattail);
return;
}
diff --git a/src/fits/fitsmisc.c b/src/fits/fitsmisc.c
index 2a035fa880c11b22d6d5799959d19ff1ae24d3f7..a149e1119a827d87bda513a55f076f94a759d084 100644
--- a/src/fits/fitsmisc.c
+++ b/src/fits/fitsmisc.c
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 09/10/2010
+* Last modified: 20/11/2013
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -40,7 +40,7 @@
#include "fitscat_defs.h"
#include "fitscat.h"
-static void (*errorfunc)(char *msg1, char *msg2) = NULL;
+static void (*errorfunc)(const char *msg1, const char *msg2) = NULL;
static char warning_historystr[WARNING_NMAX][192]={""};
static int nwarning = 0, nwarning_history = 0, nerror = 0;
@@ -48,7 +48,7 @@ static int nwarning = 0, nwarning_history = 0, nerror = 0;
/*
I hope it will never be used!
*/
-void error(int num, char *msg1, char *msg2)
+void error(int num, const char *msg1, const char *msg2)
{
fprintf(stderr, "\n> %s%s\n\n",msg1,msg2);
if (num && errorfunc && !nerror)
@@ -64,7 +64,7 @@ void error(int num, char *msg1, char *msg2)
/*
I hope it will never be used!
*/
-void error_installfunc(void (*func)(char *msg1, char *msg2))
+void error_installfunc(void (*func)(const char *msg1, const char *msg2))
{
if (func)
errorfunc = func;
diff --git a/src/fits/fitstab.c b/src/fits/fitstab.c
index 5919b2a22695f25b82c1c1f1054849179c3b8e23..a663c7ee0cb6a38cd870e475bcd0859b8b0bfcee 100644
--- a/src/fits/fitstab.c
+++ b/src/fits/fitstab.c
@@ -7,7 +7,7 @@
*
* This file part of: AstrOmatic FITS/LDAC library
*
-* Copyright: (C) 1995-2010 Emmanuel Bertin -- IAP/CNRS/UPMC
+* Copyright: (C) 1995-2023 CFHT/IAP/CNRS/SorbonneU
*
* License: GNU General Public License
*
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 11/09/2012
+* Last modified: 25/02/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -35,6 +35,10 @@
#include
#include
+#ifdef HAVE_CFITSIO
+#include CFITSIO_H
+#endif
+
#include "fitscat_defs.h"
#include "fitscat.h"
@@ -270,8 +274,8 @@ INPUT Pointer to the original catalog,
Position (1= first after the primary HDU, <=0 = at the end)
OUTPUT -.
NOTES -.
-AUTHOR E. Bertin (IAP & Leiden observatory)
-VERSION 22/06/2001
+AUTHOR E. Bertin (IAP/SorbonneU)
+VERSION 25/02/2023
***/
void copy_tab_fromptr(tabstruct *tabin, catstruct *catout, int pos)
@@ -318,6 +322,11 @@ void copy_tab_fromptr(tabstruct *tabin, catstruct *catout, int pos)
prevtab->nexttab = nexttab;
nexttab->prevtab = prevtab;
+#ifdef HAVE_CFITSIO
+ // Do not copy CFitsIO file pointer
+ tabout->infptr = NULL;
+#endif
+
return;
}
@@ -396,8 +405,8 @@ PURPOSE Free memory associated to a table pointer.
INPUT Pointer to the table.
OUTPUT -.
NOTES -.
-AUTHOR E. Bertin (IAP & Leiden observatory)
-VERSION 28/02/2000
+AUTHOR E. Bertin (CFHT/IAP/CNRS/SorbonneU)
+VERSION 25/02/2023
***/
void free_tab(tabstruct *tab)
diff --git a/src/fits/fitswrite.c b/src/fits/fitswrite.c
index a62b8c1bbce7ed7ac202053335f52eaf427113ed..6cda309c9b1340e4c9379d51f0c603e8e121354b 100644
--- a/src/fits/fitswrite.c
+++ b/src/fits/fitswrite.c
@@ -23,7 +23,7 @@
* along with AstrOmatic software.
* If not, see .
*
-* Last modified: 11/02/2020
+* Last modified: 26/08/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -359,13 +359,13 @@ INPUT catalog structure,
OUTPUT -.
NOTES -.
AUTHOR E. Bertin (IAP & Leiden observatory)
-VERSION 26/09/2004
+VERSION 03/12/2019
***/
void end_writeobj(catstruct *cat, tabstruct *tab, char *buf)
{
keystruct *key;
- OFF_T pos;
+ OFF_T2 pos;
int k;
/* Make the table parameters reflect its content*/
diff --git a/src/globals.h b/src/globals.h
index 719404c788ed760fae944f2075d452db330ef267..cabf67b81ffebfbccd7ea723c9b59c59b8eac1a1 100644
--- a/src/globals.h
+++ b/src/globals.h
@@ -22,7 +22,7 @@
* You should have received a copy of the GNU General Public License
* along with SExtractor. If not, see .
*
-* Last modified: 15/07/2020
+* Last modified: 23/09/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -82,7 +82,7 @@ extern void alloccatparams(void),
updateparamflags(void),
useprefs(void),
writecat(int, objliststruct *),
- write_error(char *msg1, char *msg2),
+ write_error(const char *msg1, const char *msg2),
write_vo_fields(FILE *file),
zerocat(void);
diff --git a/src/header.c b/src/header.c
index da03d524fa245ac502fe9c1306f66b9dd3677c80..f0514f6beea8038c05bf872d0d7a9bcfe0b857af 100644
--- a/src/header.c
+++ b/src/header.c
@@ -22,7 +22,7 @@
* You should have received a copy of the GNU General Public License
* along with SExtractor. If not, see .
*
-* Last modified: 12/07/2012
+* Last modified: 07/09/2022
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -49,7 +49,7 @@ INPUT Name of the ASCII file,
OUTPUT RETURN_OK if the file was found, RETURN_ERROR otherwise.
NOTES -.
AUTHOR E. Bertin (IAP)
-VERSION 12/07/2012
+VERSION 07/09/2022
***/
int read_aschead(char *filename, int frameno, tabstruct *tab)
{
@@ -63,7 +63,7 @@ int read_aschead(char *filename, int frameno, tabstruct *tab)
{
/*- Skip previous ENDs in multi-FITS extension headers */
for (i=frameno-1; i--;)
- while (fgets(str, MAXCHAR, file)
+ while (fgets(str, 88, file)
&& strncmp(str,"END ",4)
&& strncmp(str,"END\n",4));
memset(str, ' ', 80);
diff --git a/src/makeit.c b/src/makeit.c
index a561aaec350a277be0487ed6c7f82092ba76ac11..55c6c6b3d4f35e62104236aaa7df79319377e972 100644
--- a/src/makeit.c
+++ b/src/makeit.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2020 IAP/CNRS/SorbonneU
+* Copyright: (C) 1993-2023 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 .
*
-* Last modified: 15/07/2020
+* Last modified: 07/03/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -43,7 +43,9 @@
#include "assoc.h"
#include "back.h"
#include "check.h"
+#ifdef USE_MODEL
#include "fft.h"
+#endif
#include "field.h"
#include "filter.h"
#include "growth.h"
@@ -280,7 +282,7 @@ void makeit()
{
/*---- Check for the next valid image extension */
if ((imatab->naxis < 2)
- || !strncmp(imatab->xtension, "BINTABLE", 8)
+ || !(imatab->isTileCompressed || strncmp(imatab->xtension, "BINTABLE", 8))
|| !strncmp(imatab->xtension, "ASCTABLE", 8))
continue;
next++;
@@ -319,10 +321,9 @@ void makeit()
{
/*-- Check for the next valid image extension */
if (!forcextflag && ((imatab->naxis < 2)
- || !strncmp(imatab->xtension, "BINTABLE", 8)
+ || !(imatab->isTileCompressed || strncmp(imatab->xtension, "BINTABLE", 8))
|| !strncmp(imatab->xtension, "ASCTABLE", 8)))
continue;
-
nok++;
/*-- Initial time measurement*/
@@ -706,8 +707,8 @@ INPUT Filename character string.
OUTPUT Extension number, or RETURN_ERROR if nos extension specified.
NOTES The bracket and its extension number are removed from the filename if
found.
-AUTHOR E. Bertin (IAP)
-VERSION 08/10/2007
+AUTHOR E. Bertin (CFHT/IAP)
+VERSION 07/03/2023
***/
static int selectext(char *filename)
{
@@ -720,6 +721,7 @@ static int selectext(char *filename)
if ((bracr=strrchr(bracl+1, ']')))
*bracr = '\0';
next = strtol(bracl+1, NULL, 0);
+
return next;
}
@@ -735,9 +737,9 @@ INPUT a character string,
OUTPUT RETURN_OK if everything went fine, RETURN_ERROR otherwise.
NOTES -.
AUTHOR E. Bertin (IAP)
-VERSION 14/07/2006
+VERSION 23/09/2020
***/
-void write_error(char *msg1, char *msg2)
+void write_error(const char *msg1, const char *msg2)
{
char error[MAXCHAR];
diff --git a/src/preflist.h b/src/preflist.h
index 7273f78f3319ffdd5985a4d1cf3bdab7efae1f5a..985f0719c4546abc77fd69d96c2b25115fb4d793 100644
--- a/src/preflist.h
+++ b/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 .
*
-* 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_PEARSON", P_FLOAT, &prefs.back_pearson, 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_PEARSON 2.5 # Pearson's factor alpha >= 1 with",
+"* # (mode - mean) ~ alpha * (median - mean)",
+"* # Legacy value is 2.5, but 3.5 is more accurate",
"BACK_SIZE 64 # Background mesh: or ,",
"BACK_FILTERSIZE 3 # Background filter: or ,",
" ",
diff --git a/src/prefs.h b/src/prefs.h
index 7503438173ee2713ad05e1c13fc9ae113cfda8a2..79b016e42d603fd44ae1f49c3dc4cf52aba199b3 100644
--- a/src/prefs.h
+++ b/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 .
*
-* 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_pearson; /* Pearson's factor */
enum {GLOBAL, LOCAL} pback_type; /* phot. bkgnd type */
int pback_size; /* rect. ann. width */
/*----- memory */
diff --git a/src/readimage.c b/src/readimage.c
index f89aca11c7a8ad89b2eeaf6f03901a974b4e4eda..b2c94d0044a10791bfbc5e03e1fe2ea3b6584e3c 100644
--- a/src/readimage.c
+++ b/src/readimage.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 1993-2015 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 .
*
-* Last modified: 14/01/2015
+* Last modified: 23/09/2020
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -93,7 +93,12 @@ void *loadstrip(picstruct *field, picstruct *wfield)
else if (flags & INTERP_FIELD)
copydata(field, 0, nbpix);
else
+ {
+#ifdef HAVE_CFITSIO
+ tab->currentElement = 1;
+#endif
read_body(tab, data, nbpix);
+ }
if (flags & (WEIGHT_FIELD|RMS_FIELD|BACKRMS_FIELD|VAR_FIELD))
weight_to_var(field, data, nbpix);
if ((flags & MEASURE_FIELD) && (check=prefs.check[CHECK_IDENTICAL]))
diff --git a/src/types.h b/src/types.h
index 7903566d210829ac7cd9ba139fb96d4cdae3b089..56cfefe100caddcfb2344151d016e6a5084d5505 100644
--- a/src/types.h
+++ b/src/types.h
@@ -621,7 +621,7 @@ typedef struct pic
int interp_xtimeout; /* interpolation timeout value in x */
int interp_ytimeout; /* interpolation timeout value in y */
struct pic *reffield; /* pointer to a reference field */
- OFF_T mefpos; /* Position in a MEF file */
+ OFF_T2 mefpos; /* Position in a MEF file */
} picstruct;
diff --git a/src/xml.c b/src/xml.c
index cf1c7ce8432afe0fdf8d81f657162b23e287dc57..087f1289dee4d05d86a03bab811f18cf612b73e3 100644
--- a/src/xml.c
+++ b/src/xml.c
@@ -7,7 +7,7 @@
*
* This file part of: SExtractor
*
-* Copyright: (C) 2006-2013 Emmanuel Bertin -- IAP/CNRS/UPMC
+* Copyright: (C) 2006-2023 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 .
*
-* Last modified: 27/04/2013
+* Last modified: 07/03/2023
*
*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
@@ -231,8 +231,8 @@ INPUT Pointer to the output file (or stream),
Pointer to an error msg (or NULL).
OUTPUT RETURN_OK if everything went fine, RETURN_ERROR otherwise.
NOTES -.
-AUTHOR E. Bertin (IAP)
-VERSION 25/04/2013
+AUTHOR E. Bertin (CFHT/IAP)
+VERSION 07/03/2023
***/
int write_xml_meta(FILE *file, char *error)
{
@@ -546,6 +546,7 @@ int write_xml_meta(FILE *file, char *error)
write_xmlconfigparam(file, "BackPhoto_Type", "","meta.code;obs.param", "");
write_xmlconfigparam(file, "BackPhoto_Thick", "pix", "obs.param", "%d");
write_xmlconfigparam(file, "Back_FiltThresh", "ct", "obs.param;", "%g");
+ write_xmlconfigparam(file, "Back_Pearson", "", "obs.param;", "%g");
write_xmlconfigparam(file, "CheckImage_Type","","meta.code;obs.param", "");
write_xmlconfigparam(file, "CheckImage_Name", "",