aladin.rst

Sky Map Visualizations and Credible Regions in Aladin
=====================================================

In this section, we demonstrate working with gravitational-wave sky
localizations in `Aladin Desktop`_. The following main topics are addressed.

.. contents:: :local:

MOC and GW Sky Localizations
----------------------------

The enclosed area within a given probability level contour of a GW sky map can
be effectively described with a Multi-Order Coverage (:term:`MOC`) map
[#Fernique15]_. MOC is a standard of the Virtual Observatory which provides a
representation of arbitrary regions on the unit sphere using the
:term:`HEALPix` sky tessellation.

The MOC data structure encodes irregular sky regions as a hierarchy of HEALPix
pixels. Each MOC cell is defined by two numbers: the hierarchy level (HEALPix
:math:`\mathit{order}`) and the pixel index (HEALPix :math:`\mathit{ipix}`).
MOCs are serialized as FITS or JSON files. The finest level of refinement
within the MOC hierarchy is determined by the HEALPix :math:`\mathit{order}`
parameter or the equivalent :math:`\mathit{nside}` parameter, related by
:math:`\mathit{nside} = 2^\mathit{order}`. For example, ``order=9`` corresponds
to ``nside=512``, and a resolution of :math:`6.9'` per pixel.

The MOC maps make database queries for retrieving objects and logical operation
(such as union, intersection, subtraction, difference) extremely fast even for
very complex sky regions.

MOC maps and :doc:`multi-order sky maps </tutorial/multiorder_skymaps>` are
closely related. They use similar multi-resolution HEALPix data structures. The
main distinction is that MOC maps encode *regions on the sphere*, whereas
multi-order sky maps encode *sampled images or functions on the sphere*. The
multi-order sky map FITS format is a superset of the MOC FITS format, the only
difference being that a multi-order sky map has values attached to each cell
(probability density, distance estimates) whereas a MOC map does not. Future
Aladin releases will support the LIGO/Virgo multi-resolution sky maps.

Running Aladin Desktop
----------------------

Aladin Desktop is a Java application. To run it, you must first have the `Java
Virtual Machine`_ (JVM) installed. More details are in Aladin's `download
page`_.

.. note::
   Aladin may fail to load some LIGO/Virgo sky maps and display a
   ``java.lang.OutOfMemoryError`` error message. This is because the highest
   resolution LIGO/Virgo sky maps do not fit inside Aladin's default memory
   size.

   You can increase the maximum memory size used by your Java runtime
   environment by following the instructions below.

   Download the Aladin.jar from the Aladin `download page`_. Execute it from a
   terminal by typing::

       $ java -Xmx2g -jar Aladin.jar

   The flag ``-Xmx< ammount of memory >`` specifies the maximum memory
   allocation pool for a JVM. Here 2GB of memory is allocated. For GW sky
   localizations with ``nside=2048``, increase the memory allocated up to 3GB,
   ``-Xmx3g``.

Loading a GW Sky Localization
-----------------------------

You can copy and paste the sky map URL from the `GraceDB`_ or drag and drop a
HEALPix FITS file from your operating system's file browser in the main Aladin
window. Aladin recognizes only the standard HEALPix format with the file
extension ``.fits.gz``. Here we will work with the `LALinference sky map of
GW170817`_.

Building a Credible Region
--------------------------

The sequence of the Aladin Desktop commands to create a credible region at a
defined confidence level is described below. From the menu bar, select
:menuselection:`Coverage --> Generate a MOC based on --> The current
probability skymap`

.. figure:: /_static/aladin_fig1.png
   :alt: Create a MOC from a GW sky localization

The :guilabel:`MOC generation` window has two options: the probability sky map
and the threshold. Make sure that the GW sky map that we loaded in the previous
step is selected in the probably sky maps dropdown menu. The drop-down menu
contains the GW sky localization previously loaded and showed in the Aladin
Stack. Then enter a probability threshold between 0 and 1. Finally, press the
:guilabel:`CREATE` button. The MOC for the credible region is created and
loaded in the Aladin Stack. If you repeat this process multiple times for
different credible levels, then you can select each MOC independently from the
Aladin stack.

:guilabel:`Properties` Window
-----------------------------

To open the :guilabel:`Properties` window, right click on the selected plan in
the Aladin stack. The associated :guilabel:`Properties` windows allows to
change the drawing methods in perimeter in order to simultaneously visualize
multiple confidence levels. This operation facilitates tiling operations by
telescopes monitoring the highest probability areas. The enclosed sky area in
square degrees and the percentage of the sky coverage are quoted for each
credible region either **i)** by leaving the cursor on the corresponding plan
loaded in the Aladin stack or **ii)** by opening the associated Properties
windows.

.. figure:: /_static/aladin_fig2.png
   :alt: Properties window

You can overlap a large data set of image backgrounds provided by the `HiPS
list aggregator`_ or you can generate your own HiPS from image/cube data. For
doing this, from the main menu press :menuselection:`Tool --> Generate a HiPS
based on --> An image collections (FITS, JPEG, PNG)`

Querying and Filtering a Galaxy Catalog
---------------------------------------

Singer et al. [#Singer16b]_ discuss a fast algorithm for obtaining a
three-dimensional probability estimates of sky location and luminosity distance
from observations of binary compact object mergers with Advanced LIGO and
Virgo. Combining the reconstructed gravitational wave volumes with positions
and redshifts of possible host galaxies provides a filtered list of sky
location targets to search for the electromagnetic counterpart of the
gravitational wave signal. At present it is not implemented in Aladin a catalog
query by the GW three-dimensional posterior probability distribution. What we
can currently achieve is to query the entire galaxy catalog and, afterwards, to
filter the selection. Here a cut-distance filter is applied taking into account
the marginal distance posterior distribution integrated over the whole sky.
These tasks are efficiently performed in the Aladin Desktop using the data
collections tree and the filter methods as follows.

:menuselection:`Aladin data collections tree --> Select --> click on the
catalog item --> in the popup window check --> by region & MOC`

  .. figure:: /_static/aladin_fig3.png
   :alt:  Aladin data collection tree

Now we can filter the galaxy catalog. From the main menu press

:menuselection:`Catalog --> Create a filter--> Properties --> Advanced mode -->
Or enter your filter definition`

An example about the Aladin filter using as galaxy selection the marginal
distance posterior distribution integrated over the whole sky is reported
below: ``${Dist} > DISTMEAN-DISTSTD && ${Dist} < DISTMEAN+DISTSTD {draw}``. The
posterior mean distance (Mpc) and the posterior standard deviation of distance
(Mpc) are reported in the fits file header with the keywords ``DISTMEAN`` and
``DISTSTD``. Click on ``Apply`` and then ``Export`` to create a new plane
consisting only of sources selected by the filter.

  .. figure:: /_static/aladin_filter.png
   :alt: Aladin filter

Finally, make thumbnails of the selected galaxies. From the main menu press
:menuselection:`Tool --> Thumbnail view generator` download and select in the
Aladin stack any image background to obtain the corresponding galaxy images.

  .. figure:: /_static/aladin_fig4.png
   :alt: Thumbnail view generator

.. |apjl| replace:: *Astrophys. J. Lett.*
.. |A&A|  replace:: *Astronomy & Astrophysics*
.. |prd|  replace:: *Phys. Rev. D*

.. [#Fernique15]
   Fernique, P., Allen, et al. 2015, |A&A|, 578, A114.
   :doi:`10.1051/0004-6361/201526075`

.. [#Singer16b]
   Singer, L. P., Chen, H.-Y., Holz, D. E., et al. 2016, |apjl|, 829, L15.
   :doi:`10.3847/2041-8205/829/1/L15`

.. _`Aladin Desktop`:  https://aladin.u-strasbg.fr/AladinDesktop/
.. _`VizieR`:  http://vizier.u-strasbg.fr/index.gml
.. _`Java Virtual Machine`: https://www.java.com/en/
.. _`download page`: https://aladin.u-strasbg.fr/java/nph-aladin.pl?frame=downloading
.. _`script launcher`: https://aladin.u-strasbg.fr/java/Aladin
.. _`GraceDB`: https://gracedb.ligo.org/
.. _`LALinference sky map of GW170817`: https://dcc.ligo.org/public/0157/P1800381/006/GW170817_skymap.fits.gz
.. _`HiPS list aggregator`: https://aladin.unistra.fr/hips/list