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Commit c58d2603 authored by Giuseppe Greco's avatar Giuseppe Greco

add aladin support

fig.1 - moc window creation

Fig.2 properties window

aladin collection tree

aladin thumbnails

aladin filter

Aladin MMA

Delete Aladin_MMA.rst

Aladin tutorial

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Aladin tuto - credible regions and galaxy queries

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MOC and multi-order sky map discussion

Aladin multi-order support - future releases

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indices
interferometer
interferometers
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Kamioka
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pixelation
postprocessing
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......
Sky Map Visualizations and Credible Regions
===========================================
In this section, we demonstrate some basic strategies for 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 through the Multi-Order Coverage (MOC)
method [#Fernique15]_. It is a standard of the Virtual
Observatory which provides a multi-scale mapping based on HEALPix sky
tessellation.
The data structure maps irregular and complex sky regions into hierarchically
grouped predefined cells. Each MOC cell is defined by two numbers: the hierarchy
level (HEALPIx order) and the pixel index (HEALPIx ipix). The ``NUNIQ`` scheme
defines an algorithm for packing an (order, ipix) pair into a single integer for
compactness. MOCs are serialized as FITS or JSON files. The MOC resolution is
determined by the map resolution parameter ``nside``, which is
used for defining the resolution of the grid. For a typical
``nside=512`` (:math:`6.871'` per pixel), the MOC order resolution is
``order = 9``
.. math::
\mathit{nside} = 2^\mathit{order}.
The MOC maps make database queries for retrieving objects and logical operation
(such as union, intersection, subtraction, difference) extremely simple and fast
even for very complex sky regions. If databases are adapted to support MOC
based queries, such as `VizieR`_, they offer a useful method allowing any support
of sky region query.
The resolution of a GW sky localization with three or more detectors can reach a
resolution considerably large. To mitigate the computational time, a new variant
of the HEALPix format is designed and annotated with the file extension
``.multiorder.fits``. See the section :doc:`/tutorial/multiorder_skymaps`
for details. Although the FITS format for LIGO/Virgo multi-resolution sky maps
uses the **UNIQ** indexing scheme and is a superset of the FITS serialization for
MOC map, operationally, they are defined as follows. With *MOC map*, we
indicate the method to map complex regions for fast queries and sky map
comparisons, while, with *multi-order sky map*, we refer to a new HEALPix
format to deal with computational challenges related to highly accurate
localizations. Future Aladin releases will support the LIGO/Virgo
multi-resolution sky maps.
1. Running Aladin Desktop
-------------------------
Aladin is developed in Java. As any Java tool, Aladin Desktop requires a `Java
Virtual Machine`_ (JVM) and a classical installation on the user machine
according with your operating system.
More details in the `Download instructions`_.
.. note::
If Aladin fails during operation with a message that says something about a
``java.lang.OutOfMemoryError``, then your heap size is too small for what you
are trying to do. You will have to run Java with a bigger heap size.
You can increase the maximum memory size used by your Java runtime environment
by following the instructions below.
Download the ``Aladin.jar`` file from `here`_ and 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 Java Virtual Machine (JVM). Here 2GB of memory is
allocated. For GW sky localizations with ``NSIDE = 2048``, increase the
memory allocated up to 3GB, ``-Xmx3g``.
2. 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`_.
3. Building a Credible Region
-----------------------------
The sequence of the Aladin Desktop commands to
create a credible region at a defined confidence level is reported
below. From the main menu press
:menuselection:`Coverage --> Generate a MOC based on --> The current probability skymap --> MOC generation`
.. figure:: /_static/aladin_fig1.png
:alt: Create a MOC from a GW sky localization
The :guilabel:`MOC generation` window requires two mandatory parameters 1) the
probability sky map and 2) the threshold. The probability sky map
entry, that means the GW sky localization in our context, can be
selected from the drop-down menu. The drop-down menu contains the GW sky
localization previously loaded and showed in the Aladin Stack. The threshold
input represents the percentage of the credible region in decimal
(ranging from 0 to 1). Press the :guilabel:`CREATE` button to generate the
resulting credible region. The credible region is created and loaded in
the Aladin Stack. The credible region obtained so far are decoded in the
Multi Order Coverage map (MOC) and each new level can be independently
used.
4. :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)`
5. 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 instructions`: https://aladin.u-strasbg.fr/java/nph-aladin.pl?frame=downloading
.. _`here`: 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
\ No newline at end of file
......@@ -22,3 +22,4 @@ tutorial is broken into the following subsections:
observability
3d
tools
aladin
......@@ -118,7 +118,7 @@ Aladin_:
:alt: Aladin screenshot
or DS9_ (although DS9 shows HEALPix sky maps in an unusual orientation; see
Figure 4 of [#MappingOnHEALPix]_ for more information.
Figure 4 of [#MappingOnHEALPix]_ for more information.
.. image:: /_static/ds9-screenshot.png
:alt: DS9 screenshot
......
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