@@ -12,95 +14,68 @@ is not necessary to operate the software.
Memory requirements depend on the size of the images to be processed.
Memory requirements depend on the size of the images to be processed.
Processing a single image should typically require about 100MB of memory.
Processing a single image should typically require about 100MB of memory.
For large images (hundreds of Mpixels or more), or in double-image / weighted
For large images (hundreds of Mpixels or more), or in double-image / weighted mode, |SExtractor|'s memory footprint should be around 500MB, and up to 2GB in the worst cases.
mode, |SExtractor|'s memory footprint should be around 500MB, and up to 2GB in
Swap-space can be put to contribution, although a strong performance hit is to be expected.
the worst cases. Swap-space can be put to contribution, although a strong
performance hit is to be expected.
Obtaining |SExtractor|
Obtaining |SExtractor|
----------------------
----------------------
For Linux users, the simplest way to have |SExtractor| up and running is to
For Linux users, the simplest way to have |SExtractor| up and running is to install the standard binary package the comes with your Linux distribution.
install the standard binary package the comes with your Linux distribution.
Run, e.g., ``apt-get sextractor`` (on Debian) or ``dnf sextractor`` (Fedora) as root and |SExtractor|, as well as all its dependencies, will automatically be installed.
Run, e.g., ``apt-get sextractor`` (on Debian) or ``dnf sextractor`` (Fedora) as
If you decided to install the package this way you may skip the following and move straight to the :ref:`next section <Using Sextractor>`.
root and |SExtractor|, as well as all its dependencies, will automatically be
installed. If you decided to install the package this way you may skip the
However if |SExtractor| is not available in your distribution, or to obtain the most recent version, the |SExtractor| source package can be downloaded from `the official GitHub repository <https://github.com/astromatic/sextractor>`_ .
following and move straight to the :ref:`next section <Using Sextractor>`.
One may choose `one of the stable releases <https://github.com/astromatic/sextractor/releases>`_, or for the fearless, `a copy of the current master development branch <https://github.com/astromatic/sextractor/archive/master.zip>`_.
However if |SExtractor| is not available in your distribution, or to obtain the
most recent version, the |SExtractor| source package can be downloaded from
`the official GitHub repository <https://github.com/astromatic/sextractor>`_ .
One may choose `one of the stable releases
<https://github.com/astromatic/sextractor/releases>`_, or for the fearless,
|SExtractor| has been developed on `GNU/Linux <http://en.wikipedia.org/wiki/Linux>`_ machines and should compile on any `POSIX <http://en.wikipedia.org/wiki/POSIX>`_-compliant system (this includes |OSX|_ and `Cygwin <http://www.cygwin.com>`_ on |Windows|_, at the price of some difficulties with the configuration), provided that the *development* packages of the following libraries have been installed:
`GNU/Linux <http://en.wikipedia.org/wiki/Linux>`_ machines and should compile on
any `POSIX <http://en.wikipedia.org/wiki/POSIX>`_-compliant system (this
includes |OSX|_ and `Cygwin <http://www.cygwin.com>`_ on |Windows|_, at the
price of some difficulties with the configuration), provided that the
*development* packages of the following libraries have been installed:
* |ATLAS|_ V3.6 and above [#atlas_install]_,
* |ATLAS|_ V3.6 and above [#atlas_install]_,
* |FFTw|_ V3.0 and above [#fftw_install]_,
* |FFTw|_ V3.0 and above [#fftw_install]_,
On Fedora/Redhat distributions for instance, the development packages above are
On Fedora/Redhat distributions for instance, the development packages above are available as ``atlas-devel`` and ``fftw-devel``.
available as ``atlas-devel`` and ``fftw-devel``. Note that |ATLAS| and |FFTw|
Note that |ATLAS| and |FFTw| are not necessary if |SExtractor| is linked with |Intel|'s |MKL|_ library.
are not necessary if |SExtractor| is linked with |Intel|'s |MKL|_ library.
Installation
Installation
------------
------------
To install from the |GitHub| source package, you must first uncompress the
To install from the |GitHub| source package, you must first uncompress the archive:
archive:
.. code-block:: console
.. code-block:: console
$ unzip sextractor-<version>.zip
$ unzip sextractor-<version>.zip
A new directory called :file:`sextractor-<version>` should now appear at the
A new directory called :file:`sextractor-<version>` should now appear at the current location on your disk.
current location on your disk. Enter the directory and generate the files
Enter the directory and generate the files required by the `autotools <http://en.wikipedia.org/wiki/GNU_Build_System>`_, which the package relies on:
required by the `autotools <http://en.wikipedia.org/wiki/GNU_Build_System>`_,
which the package relies on:
.. code-block:: console
.. code-block:: console
$ cd sextractor-<version>
$ cd sextractor-<version>
$ sh autogen.sh
$ sh autogen.sh
A :program:`configure` script is created. This script has many options, which
A :program:`configure` script is created.
may be listed with the ``--help`` option:
This script has many options, which may be listed with the ``--help`` option:
.. code-block:: console
.. code-block:: console
$ ./configure --help
$ ./configure --help
No options are required for compiling with the default GNU C compiler
No options are required for compiling with the default GNU C compiler (:program:`gcc`) if all the required libraries are installed at their default locations:
(:program:`gcc`) if all the required libraries are installed at their default
locations:
.. code-block:: console
.. code-block:: console
$ ./configure
$ ./configure
Compared to :program:`gcc` and the librairies above, the combination of the
Compared to :program:`gcc` and the librairies above, the combination of the |Intel| compiler (:program:`icc`) and the |MKL|_ libraries can give the |SExtractor| executable a strong boost in performance, thanks to better vectorized code.
|Intel| compiler (:program:`icc`) and the |MKL|_ libraries can give the
If :program:`icc` and the |MKL| are installed on your system [#geticc]_ , you can take advantage of them using
|SExtractor| executable a strong boost in performance, thanks to better
vectorized code. If :program:`icc` and the |MKL| are installed on your system
[#geticc]_ , you can take advantage of them using
.. code-block:: console
.. code-block:: console
$ ./configure --enable-mkl
$ ./configure --enable-mkl
Additionally, if the |SExtractor| binary is to be run on a different machine
Additionally, if the |SExtractor| binary is to be run on a different machine that does not have :program:`icc` and the |MKL| installed (e.g., a cluster computing node), you must configure a partially statically linked executable using
that does not have :program:`icc` and the |MKL| installed (e.g., a cluster
computing node), you must configure a partially statically linked executable
using
.. code-block:: console
.. code-block:: console
@@ -112,34 +87,22 @@ In all cases, |SExtractor| can now be compiled with
$ make -j
$ make -j
An :file:`src/sex` executable is created. For system-wide installation, run
An :file:`src/sex` executable is created. For system-wide installation, run the usual
the usual
.. code-block:: console
.. code-block:: console
$ sudo make install
$ sudo make install
You may now check that the software is properly installed by simply
You may now check that the software is properly installed by simply typing in your shell:
typing in your shell:
.. code-block:: console
.. code-block:: console
$ sex
$ sex
which will return the version number and other basic information (note that
which will return the version number and other basic information (note that some shells require the :program:`rehash` command to be run before making a freshly installed executable accessible in the execution path).
some shells require the :program:`rehash` command to be run before making a
freshly installed executable accessible in the execution path).
.. [#mac_install] Mac OS X |.dmg|_ packages should be available soon.
.. [#mac_install] Mac OS X |.dmg|_ packages should be available soon.
.. [#atlas_install] Use the ``--with-atlas`` and/or
.. [#atlas_install] Use the ``--with-atlas`` and/or ``--with-atlas-incdir`` options of the |SExtractor| :command:`configure` script to specify the |ATLAS| library and include paths if |ATLAS| files are installed at unusual locations.
``--with-atlas-incdir`` options of the |SExtractor| :command:`configure`
.. [#fftw_install] Make sure that |FFTW| has been compiled with :command:`configure` options ``--enable-threads --enable-float``.
script to specify the |ATLAS| library and include paths if |ATLAS| files are
.. [#geticc] The Linux versions of the |Intel| compiler and |MKL| are `available for free to academic researchers, students, educators and open source contributors <http://software.intel.com/qualify-for-free-software>`_.
installed at unusual locations.
.. [#fftw_install] Make sure that |FFTW| has been compiled with
|SExtractor|_ (Source-Extractor) is a program that builds a catalog
|SExtractor|_ (Source-Extractor) is a program that builds a catalog of objects from an astronomical image. It is particularly oriented towards the reduction of large scale galaxy-survey data, but it also performs well on moderately crowded star fields. Its main features are:
of objects from an astronomical image. It is particularly oriented
towards the reduction of large scale galaxy-survey data, but it also performs
well on moderately crowded star fields. Its main features are:
* Support for multi-extension FITS (|MEF|_)
* Support for multi-extension FITS (|MEF|_)
* Speed: up to about 50 Mpixel/s or 10,000 sources/s with a 3 GHz processor
* Speed: up to about 50 Mpixel/s or 10,000 sources/s with a 3 GHz processor
@@ -22,8 +21,5 @@ well on moderately crowded star fields. Its main features are:
* Built-in catalog cross-identification.
* Built-in catalog cross-identification.
* Special mode for photographic scans.
* Special mode for photographic scans.
* |XML|_ |VOTable|_-compliant catalog output.
* |XML|_ |VOTable|_-compliant catalog output.
* |XSLT|_ filter sheet provided for convenient access to metadata from a
* |XSLT|_ filter sheet provided for convenient access to metadata from a regular web browser.
|SExtractor|_ *is free software: you can redistribute it and/or modify it under
|SExtractor|_ *is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.*
the terms of the GNU General Public License as published by the Free
|SExtractor| *is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Software Foundation, either version 3 of the License, or (at your
See the GNU General Public License for more details.
option) any later version.* |SExtractor| *is distributed in the hope that it will
You should have received a copy of the GNU General Public License along with* |SExtractor|. *If not, see* `www.gnu.org/licenses/ <http://www.gnu.org/licences/>`_.
be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details. You should have received a copy
of the GNU General Public License along with* |SExtractor|. *If not, see*
Once sources have been detected and deblended, they enter the measurement phase. |SExtractor| performs three categories of measurements: isophotal, full, and model-fitting.
.. include:: global.rst
Once sources have been detected and deblended, they enter the measurement phase.
|SExtractor| performs three categories of measurements: isophotal, full, and model-fitting.
.. _isophotal_measurements:
.. _isophotal_measurements:
Isophotal
Isophotal
Measurements are made on the isophotal object footprints, which are defined on the filtered detection image. Only pixels with values above the threshold set with ``ANALYSIS_THRESH`` are considered [#thresh]_, which makes the analysis extremely fast, but obviously strongly dependent on the threshold itself. This is an issue particularly when the amplitude of the bakground noise varies over the image. Many of the isophotal measurements (e.g., ``X_IMAGE``, ``Y_IMAGE``, ``FLUX_ISO``) are necessary for the internal operations of |SExtractor| and are therefore executed even if they are not requested.
Measurements are made on the isophotal object footprints, which are defined on the filtered detection image. Only pixels with values above the threshold set with ``ANALYSIS_THRESH`` are considered [#thresh]_, which makes the analysis extremely fast, but obviously strongly dependent on the threshold itself. This is an issue particularly when the amplitude of the bakground noise varies over the image. Many of the isophotal measurements (e.g., :param:`X_IMAGE`, :param:`Y_IMAGE`, :param:`FLUX_ISO`) are necessary for the internal operations of |SExtractor| and are therefore executed even if they are not requested.
Full
Full
Measurements have access to all pixels of the image. These measurements are generally more sophisticated, less affected by variable biases induced by the detection threshold, and still reasonably fast. They are done at a later stage of the processing, after CLEANing and MASKing.
Measurements have access to all pixels of the image. These measurements are generally more sophisticated, less affected by variable biases induced by the detection threshold, and still reasonably fast. They are done at a later stage of the processing, after CLEANing and MASKing.
@@ -23,5 +26,4 @@ Model-fitting
.. [#thresh] Pixel values also have to exceed the local detection threshold set with ``DETECT_THRESH``.
.. [#thresh] Pixel values also have to exceed the local detection threshold set with ``DETECT_THRESH``.
.. [#psf_models] PSF models be computed using the |PSFEx|_ package.
.. [#psf_models] PSF models be computed using the |PSFEx|_ package.
