cdstutorial_4ESCAPE.tex

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\begin{document}
% First provide initial author and their affiliation as well as the
% title of the tutorial
\author{Mark Allen and the CDS team \\      % Authors
Centre de Donn\'ees astronomiques de Strasbourg, France}       % Affiliation
\title{An introduction to the \\ CDS services and tools}   % Tutorial title
\makeescapetitle

\newpage
% For every notable step forward of this tutorial, provide the name of
% the authors and their contribution here to track the development of the
% tutorial. This is always followed by \addescapehistory, which will add
% the information to the file.
\author{Mark Allen and the CDS team}   % Author
\title{Initial development of the tutorial}  % Contribution
\addescapehistory
\author{Jenny G. Sorce}
\title{updated with a new template for ASTERICS with the new CDS portal, new plots}
\addescapehistory
\author{Katharina A. Lutz}
\title{updated to \aladin\ v10}
\addescapehistory
\author{Ada Nebot}
\title{updated for VO school in Nice, November 2019}
\addescapehistory
\author{Katharina A. Lutz}
\title{updated to \aladin\ v11 and ESCAPE template}
\addescapehistory
\newpage
% Add a table of contents
\tableofcontents

\newpage
% Main body of the tutorial begins here. Generally the tutorials contain
% an introduction, which details the goals of this tutorial and provide infor-
% mation on which software packages are required. Otherwise the style is free.
\section{Introduction}

The CDS hosts three major services, accessible through the CDS portal:\\
\begin{itemize}
\item \includegraphics[width=0.1 \textwidth]{../images/logo_simbad.png}
\textbf{\simbad}: The astronomical database \simbad\ contains more than
12 million objects. For each object it provides basic measurements (type,
coordinates, proper motion, radial velocity, spectral type, distance,
magnitude), cross-correlations and bibliography.
\item \includegraphics[width=0.08 \textwidth]{../images/logo_vizier.png}
\textbf{\vizier}: The \vizier\ catalogue service provides access to more than
20,000 catalogues, being the most complete library of published astronomical
data tables available online.
\item \includegraphics[width=0.1  \textwidth]{../images/logo_aladin.png}
\textbf{\aladin}: The interactive sky atlas \aladin\ allows to
visualize astronomical images and to superimpose entries from different
catalogues and databases. It allows to visualize data from \simbad, \vizier, and
from archives and databases distributed around the world. Furthermore, you can
open your own tables or images. There are two versions of \aladin: Aladin desktop and Aladin
Lite, which runs in the browser.
\end{itemize}

In addition, the CDS has been offering a cross-match service
(X-match \includegraphics[width=0.06
\textwidth]{../images/logo_xmatch_new.png} ) since November 2011.

\section{Goal of this tutorial}

This tutorial shows how to use the CDS tools to gather information on
specific astronomical objects. We will:
\begin{itemize}
\item Search for information on NGC4039 in the CDS portal
\item Search for data concerning NGC4039 in \aladin\
\item Compare the coverage of Sky Surveys and select interacting
galaxies that have SDSS and GALEX data
\end{itemize}

\section{Search for information on NGC4039 in the CDS Portal}

Open the \href{http://cdsportal.u-strasbg.fr/}{\textcolor{blue}{CDS Portal}}
and make a query for `NGC4039'.
The result provides an overview of the information and data available for
this object in the 3 CDS services: \simbad, \aladin\ and \vizier:

\begin{figure}[H]
\center
\includegraphics[width=0.5  \textwidth]{../images/cdsportal_search_ngc4039.jpg}
\caption{Query for NGC4039 in the CDS Portal}
\label{fig:cdsportal1}
\end{figure}

\subsection{\simbad\ - Identifiers, Basic Measurements and links to the
Bibliography}

\begin{figure}[H]
    \center
    \includegraphics[width=1
    \textwidth]{../images/cdsportal_object-information_ngc4039.png}
    \caption{Result of the query for NGC4039 in the CDS Portal}
    \label{fig:cdsportal2}
\end{figure}

\begin{itemize}
    \item Click on \textbf{More info in Simbad} to see the full \simbad\
information on this object in a new tab.
\begin{figure}[H]
    \center
    \includegraphics[width=1
    \textwidth]{../images/simbad_section_basic-data.png}
    \caption{Result of the query for NGC4039 in \simbad.}
    \label{fig:simbad}
\end{figure}
    \item Note the list of \textbf{Other object types}. These types are
drawn for the literature and are stored in \simbad\ using a
hierarchical classification scheme. The full list of Object Types can
be found here:
\href{http://simbad.u-strasbg.fr/simbad/sim-display?data=otypes}
{\textcolor{blue}{http://simbad.u-strasbg.fr/simbad/sim-display?data=otypes}}.
The main Object Type of NGC4039 is \textbf{Galaxy in Pairs of Galaxies
(GiP)}.
    \item Use the {\bf parents} button \includegraphics[width=0.07
\textwidth]{../images/simbad_button_parents.png} to identify the name
of the galaxy pair. Sorting by the number of references
\includegraphics[width=0.04  \textwidth]{../images/simbad_sort_references.jpg}
can help bring out the most important ones.
    \item Follow the link to the \simbad\ entry of the Antennae galaxy pair
\includegraphics[width=0.07
\textwidth]{../images/simbad_antennae-galaxt-pair_link.png}. There
click on the {\bf children} button \includegraphics[width=0.07
\textwidth]{../images/simbad_button_children.png} to identify the name
of the two galaxies making up the galaxy pair. Again the number of references
might help to find them.
    \item Visit the \simbad\ entry of the interaction partner of NGC\,4039 and
use the {\bf References} section to find the earliest listed reference in the
literature to this object.
% this would be in 1923 ( 1923ApJ....57..137D )
\begin{figure}[H]
    \center
    \includegraphics[width=1
    \textwidth]{../images/simbad_section_references.png}
    \caption{References section}
    \label{fig:simbad_references}
\end{figure}

    \item Return to the CDS portal.
\end{itemize}




\subsection{\aladin\ - Images}


\begin{figure}[H]
\center
\includegraphics[width=1
\textwidth]{../images/cdsportal_image-information_ngc4039.png}
\caption{Result of the query for NGC4039 in the CDS Portal}
\label{fig:cdsportal3}
\end{figure}

\begin{itemize}
\item A DSS (Digitized Sky Survey) image of NGC4039 is shown.
\item Note that you can zoom in and out by scrolling your mouse when the mouse
pointer is positioned on top of the images.
\item Other images can be displayed by selecting them in the left
column. Select the PanSTARRS DR1 and 2MASS colour images one after another to
see a higher resolution image and an image at infrared wavelength of the galaxy
pair.
\item Filtering on wavelength and resolution is possible by
ticking/unticking the boxes in that same column.
\end{itemize}


\subsection{\vizier\ - Catalogues}


\begin{figure}[H]
\center
\includegraphics[width=1
\textwidth]{../images/cdsportal_catalogue-information_ngc4039.png}
\caption{Result of the query for NGC4039 in the CDS Portal}
\label{fig:cdsportal4}
\end{figure}

\begin{itemize}
\item The list of catalogues is sorted by \textbf{Popularity} but can
also be sorted by number of rows (\textbf{\#rows}), \textbf{sky
fraction} or \textbf{year}.
\item Restrictions and filtering can be applied by clicking
on the left or right columns according to your requirements. How many catalogues
provide data in the optical for galaxies and come with images as associated data?
% that would be 2 catalogues
Now go back to displaying all catalogues available within 0.2\,deg of NGC4039 by
clicking the
\includegraphics[width=0.06  \textwidth]{../images/cdsportal_show_all.png} button.
\item After selecting one catalogue, it is possible to look at it it (either
quickly \includegraphics[width=0.06  \textwidth]{../images/cdsportal_quickview.png}
or in \vizier\ \includegraphics[width=0.03 \textwidth]{../images/cdsportal_vizier.png}),
to plot column values \includegraphics[width=0.05 \textwidth]{../images/cdsportal_plot.png}
and to send it to \aladin\ (or other SAMP-aware tools like TOPCAT)
\includegraphics[width=0.03 \textwidth]{../images/cdsportal_samp.png}.
\begin{figure}[H]
\center
\includegraphics[width=1 \textwidth]{../images/cdsportal_table_usno.jpg}
\caption{Selection of a \vizier\ Catalogue on the CDS Portal.}
\label{fig:cdsportal5}
\end{figure}
\item Actually the Antennae is listed in the Arp Atlas of Peculiar
Galaxies, search for this catalogue by typing 'Arp' into the \textbf{Search} box.

\begin{figure}[H]
\center
\includegraphics[width=0.6
\textwidth]{../images/cdsportal_search-table_arp.jpg}
\caption{Looking for `Arp' in the \vizier\ catalogues.}
\label{fig:arp}
\end{figure}
\item There are two tables for Webb 1996. Using the info button
\includegraphics[width=0.03 \textwidth]{../images/cdsportal_info.png}, you'll
see that the \textbf{arplist} table contains a list of all galaxies with some
additional information. Select the \textbf{arplist}
table by clicking on it and then on \includegraphics[width=0.05
\textwidth]{../images/logo_vizier.png}. This sends to the \vizier\ detailed
query page.
\item Make a first query on this table by clicking on \textbf{submit}.
Examine the output as html. Go back to the previous page.
\item Modify the query preferences to add extra coordinate columns in
J2000 decimal degrees and to obtain the whole catalogue:
\begin{itemize}
    \item Remove the restriction on searching only around `NGC4039' by clicking
    on the \textbf{Clear} button below \textbf{Target Name (resolved by
        Sesame) or Position} at the top of the page.
    \item In \textbf{Preferences} on the left side of the page, add extra
    coordinate columns in decimal degrees by ticking \textbf{J2000} and
    \textbf{decimal} boxes.
    \item Change the maximum (\textbf{max}) number of rows to
    \textbf{unlimited} and tick \textbf{All columns} to get the whole
    catalogue.
    \begin{figure}[H]
        \center
        \includegraphics[width=0.2
        \textwidth]{../images/vizier_preferences.jpg}
        \caption{\textbf{Preferences} panel.}
        \label{fig:pref}
    \end{figure}
    \item Submit again.
\end{itemize}
\end{itemize}
The following steps are optional for the workflow of this tutorial, but they
might come in handy for other problem sets.
\begin{itemize}
\item When satisfied, click on \textbf{Save in CDSportal}, then click
on the \textbf{Save} button. The file is now saved in your personal
user space on the CDS portal. \includegraphics[width=0.1
\textwidth]{../images/vizier_saveto_CDSportal.png}
\item Click on \textbf{Go to MyData} and download a copy in
\textbf{VOTable} format on your desktop. This file can be used later
in the tutorial.
\begin{figure}[H]
\center
\includegraphics[width=1  \textwidth]{../images/cdsportal_mydata.jpg}
\caption{Personal User Space on the CDS Portal.}
\label{fig:download}
\end{figure}
\end{itemize}

\subsection{How do the data get into the CDS databases?}
As you have seen in the last sections, the CDS databases (\simbad, \vizier, the
HiPS server for images) host large amounts of a variety of data products. To provide these data to the astronomical community, about 12 data stewards curate the data. This involves collecting
data from journal papers, receiving data directly from large surveys (such as
e.\,g. Gaia), assessing and assuring the data quality and cross-matching
sources described by newly published papers/data with sources already available
in the databases. You can make this a smooth process by making sure that all
sources in your papers appear with correct coordinates and names already known
by \simbad.

\section{Search for data on NGC4039 in \aladin}

Open \aladin\ with at least 1GB memory allocated to the save virtual
machine. To do so use the following command line: \texttt{java -Xmx1024m -jar
Aladin.jar}

Aladin offers two ways to retrieve data: through the \textsc{Data Tree} on the
left hand side of the \aladin\ window and through the
\textsc{Server Selector} window, which can be opened via \textbf{File
$\rightarrow$ Open server selector...} or with \textbf{CTRL + l}.

Data sets in the \textsc{Data Tree} are colour coded in green or orange
depending on whether or not they are available in the region currently visible
in the main viewing window.

\begin{figure}[H]
    \centering
    \begin{subfigure}[H]{0.4\textwidth}
        \center
        \includegraphics
            [width=0.4\textwidth]
            {../images/aladin_data_discovery_tree_open.png}
        \caption{The \textsc{Data Tree}: green entries are available for the
        sky region currently visible in the main viewing window (not shown).}
        \label{fig:data_disc_tree}
    \end{subfigure}
    \centering
    \begin{subfigure}[H]{0.4\textwidth}
        \center
        \includegraphics[width=1
        \textwidth]{../images/aladin_server_selector.png}
        \caption{The \textsc{Server Selector} window: here \simbad\ has been
        queried for galaxies within 14\,arcmin around NGC\,4093.}
        \label{fig:server_selector}
    \end{subfigure}
    \caption{The two entry points to retrieving data in Aladin: The
    \textsc{Data Tree} (left) and the \textsc{Server Selector} (right).}
\end{figure}

\begin{itemize}
    \item Start by typing "NGC4039" in the \textbf{Command} line
\includegraphics[width=0.2\textwidth]{../images/aladin_command_ngc4039.png}
and press \textbf{Enter}. In the main viewing window the coloured DSS image of
the Antennae galaxies appears. As for the \aladin\ Lite window in the CDS
portal you can zoom in and out by scrolling your mouse.

    \item Make a contour map of the image using the \textbf{cont} button
\includegraphics[width=0.03  \textwidth]{../images/aladin_button_contours.png}
next to the main viewing window. Increase the number of contours to better
represent the image.

    \item Overlay a \simbad\ plane showing only the galaxies by selecting
the \includegraphics[width=0.055 \textwidth]{../images/logo_simbad.png} tab
in the \textsc{Server selector} and choosing \textbf{Galaxy} as the \textbf{Display
filter} (see Figure~\ref{fig:server_selector}).

    \item Change the colour of the \simbad\ plane using the button
\textbf{Properties}
\includegraphics[width=0.03\textwidth]{../images/aladin_button_properties.png}.


    \item Using the \textbf{Select} tool \includegraphics[width=0.03
\textwidth]{../images/aladin_button_select.png}, select some of the \simbad\
points either by clicking on one point or by holding the left mouse button and
drawing a rectangle. The sources within the rectangle are then selected and
displayed as a table below the image. This window can be detached with the icon
\includegraphics[width=0.035
\textwidth]{../images/aladin_button_detach-table.png} in the bottom right
corner of the table window. Note that the data point
belonging to a row in the table blinks in the main viewing window when
hoovering over the table row with the mouse.

    \item In the \textsc{Data Tree}, go to \textbf{Images $\rightarrow$
Infrared $\rightarrow$ 2MASS} and load the 2MASS colour image. To do so click on
the 2MASS colour image entry and the loading window appears (see
Figure~\ref{fig:aladin_load_2mass}). In the loading window, check that the box
for progressive loading is ticked \includegraphics[width=0.07
\textwidth]{../images/aladin_load_progessive.png} and load the image by
clicking \textbf{Load} \includegraphics[width=0.07
\textwidth]{../images/aladin_load_load.png}.

\begin{figure}[H]
    \center
    \includegraphics[width=1
    \textwidth]{../images/aladin_load_2mass-rgb-image.png}
    \caption{Loading the 2MASS colour image from the \textsc{Data Tree}. }
    \label{fig:aladin_load_2mass}
\end{figure}

    \item Once the 2MASS image is loaded it appears in the stack, which is
    located to the right of the main viewing window. The stack informs you of
    all planes that are currently loaded into \aladin. These layers are shown
    in the main viewing window as if you were looking from top to bottom
    through the stack. As it was most recently loaded, the 2MASS plane is now shown
    as the "background" image in the main viewing window. If you want to go
    back to the DSS colour image being the "background" image, tick the little
    grey box next to the DSS image entry in the stack. If you now use the
    opacity slider \includegraphics[width=0.035
    \textwidth]{../images/aladin_button_opacity.png} next to the 2MASS plane in
    the image stack, you can change the opacity of the 2MASS plane and thus compare
    it easily to the DSS image. If you wanted to overlay the DSS image on the
    2MASS image, you would have to change their order in the stack by drag-and-drop.

    \item Now add more colour images form the \textsc{Data Tree}, for example
the allWISE (infrared) and the XMM Newton (X-rays) colour images. Compare the
images in a number of different ways:
    \begin{itemize}
        \item Multiview: \textbf{View $\rightarrow$ Create one view per image},
        or via the \textbf{multiview} icon at the bottom left of the \aladin\
        image window \includegraphics[width=0.1
        \textwidth]{../images/aladin_button_multiview.jpg}. After selecting
        e.\,g. the four by four grid drag and drop the images into the panels,
        where you want to see them.
        \item Align and scale all images by using the \textbf{match} icon below
        the image window \includegraphics[width=0.04
        \textwidth]{../images/aladin_button_match-views.jpg}.
        \item Transparency overlays: return to single view mode. Change the
        transparency of planes in the stack with the opacity sliders
        \includegraphics[width=0.04
        \textwidth]{../images/aladin_button_opacity.png} as before. Remember
        that you can move the location of the planes in the stack and thus
        change the order in which the image are shown.
    \end{itemize}

    \item All the colour images we have loaded so far are pre-computed. \aladin\
    also allows you to compute your own RGB colour images:
     \begin{itemize}
         \item For this task, we need fits images rather than the HiPS tiles we have
         worked with so far. Those fits images may come from your own data or
         from the Virtual Observatory. We will now search and load images at
         the location of the Antennae galaxies from the VO using the simple image
         access (SIA) protocol.
         \item First, we look for a far-ultraviolet image from
         \textit{GALEX}: Enter "GALEX Atlas of nearby galaxies" in the
         \textbf{Select} line below the
         \textsc{Data Tree} \includegraphics[width=0.17
         \textwidth]{../images/aladin_select_GALEX.png}. In the \textsc{Data
         Tree} you will find the entry "GALEX Atlas of nearby galaxies" under
         \textbf{Others} $\rightarrow$ \textbf{SIA (image)} $\rightarrow$
         \textbf{mast.stsci}. Load this entry \textbf{in view}
         \includegraphics[width=0.07 \textwidth]{../images/aladin_load_inview.png}.
         A table appears in the stack.
         \item The newly loaded table contains a row for every image available
         from this image service in the vicinity of NGC\,4039. Find the entry
         for the file "h\_ngc4038-fd-int.fits.gz" and click on the URL in the
         first column. This will load the corresponding fits image into your
         stack.
%         \item Empty the \textbf{Select} line and repeat the steps from above
%         to load a $R$-band image from the Digitised Sky Survey: go to
%         \textbf{Others} $\rightarrow$ \textbf{SIA (image)} $\rightarrow$
%         \textbf{eso.org} and load the table of observations of the
%         \textbf{Digitized Sky Survey}. In the newly loaded table select the
%         row with "SurveyName" "DSS2-red" and load the corresponding image
%         from
%         the URL in the first column.
         \item Next, we are after an infrared image: search for "2MASS large
         galaxy atlas" in the \textbf{Select} line, load the table from
         \textbf{Others} $\rightarrow$ \textbf{SIA (image)} $\rightarrow$
         \textbf{irsa.ipac} $\rightarrow$ \textbf{2MASS Large Galaxy Atlas}
         and select any one of the three entries in the
         table to load into the stack.
         \item Finally let's add an X-ray image to the collection: search for
         "Chandra X-ray Observatory" in the \textbf{Select} line. There will be
         two services available, we will want to use the SIA service. Load the
         table "in view" from
         \textbf{Others} $\rightarrow$ \textbf{SIA (image)} $\rightarrow$
         \textbf{cxc.harvard.edu} $\rightarrow$
         \textbf{Chandra X-ray Observatory Data Archive} and select one of the
         observations with the longest "exptime".
         \item To create the RGB image, open the \textbf{RGB image generator}
         with \includegraphics[width=0.04
         \textwidth]{../images/aladin_button_rgb.png} (see
         Figure~\ref{fig:aladin_rgb_generator}). Enter the images you want to
         use for each colour component and click \textbf{CREATE}. If you want
         to adjust flux scale and transfer function of the individual images, use
         the \textbf{pixel} \includegraphics[width=0.04
         \textwidth]{../images/aladin_button_pixel.png} menu.
     \end{itemize}

\begin{figure}[H]
    \centering
    \begin{subfigure}[H]{0.4\textwidth}
        \center
        \includegraphics
        [width=\textwidth]
        {../images/aladin_rgb_window.png}
        \caption{The RGB image generator window. }
           \label{fig:aladin_rgb_generator}
       \end{subfigure}
       \centering
       \begin{subfigure}[H]{0.4\textwidth}
           \center
           \includegraphics[width=1
           \textwidth]{../images/aladin_results_rgb_image.png}
           \caption{The resulting RGB image for the Antennae galaxies. }
           \label{fig:rgb_image}
       \end{subfigure}
       \caption{Creating RGB images in \aladin.}
   \end{figure}

    \item Search for more data from the VO on NGC4039:
    \begin{itemize}
        \item To restrict the collections that the \textsc{Data Tree} is
        showing, use the \textbf{Select} line below the
        \textsc{Data Tree} \includegraphics[width=0.1
        \textwidth]{../images/aladin_select_transient.png}. For example when
        searching for transients within
        the Antennae galaxies you might restrict the search to "transient" and
        find that the Palomar Transient Factory photometric catalogue has data
        for transient events in the area. Load the catalogue and find the data
        points in the main viewing window.
        \item More elaborate filters can be created using the \textbf{Data
        Discovery Tree Filter} window, accessed through
        \includegraphics[width=0.04
        \textwidth]{../images/aladin_button_filtertree.png} next to the
        \textbf{Select} line.
        \item As before, entries in the \textsc{Data Tree}, which are coloured
        in green, have data available in the region currently visible in the
        main viewing window.
    \end{itemize}
    \item Now delete all the planes in your stack before continuing. This is
    not mandatory but it will free some useful memory space and allow you to
    proceed more easily with the next steps.
\end{itemize}
\begin{figure}[H]
\center
\includegraphics[width=0.7
\textwidth]{../images/aladin_results_cdstutorial-sec4.png}
\caption{Results of all the above mentioned steps.}
\label{fig:aladinNGC4039}
\end{figure}


\section{Compare the coverage of Sky Surveys and select interacting
galaxies that have SDSS and GALEX data}

Many large sky surveys in \aladin\ are stored in the \textbf{HiPS} format
(\href{http://aladin.u-strasbg.fr/hips/}{\textcolor{blue}
	{Hierarchical Progressive Survey}}),
which allows for easy access, browsing and visualisation of image and catalogue
data. To describe (non-trivially shaped) regions on the sky \textbf{MOC}
(Multi-Order Coverage) maps are used. In the following, we will make use of the
advantages of these two data structures to easily asses which galaxies in the
Arp catalogue of peculiar galaxies have been observed by SDSS and GALEX. If you
would like to have an overview of currently available HiPS, have a look at
\href{https://aladin.u-strasbg.fr/hips/list}{\textcolor{blue}
	{this list}}. You can load any of them in
\aladin\ by entering their base URL in the \textbf{Command} line.

\begin{itemize}
    \item Select the \textbf{SDSS 9 colored} (\textbf{Image $\rightarrow$
Optical $\rightarrow$ SDSS}) and \textbf{GALEX All Sky Imaging Survey
colored} (\textbf{Image $\rightarrow$ UV $\rightarrow$ GALEX}) surveys in the
\textsc{Data Tree} and load both the imaging data (tick progressive
\includegraphics[width=0.1\textwidth]{../images/aladin_load_progessive.png})
and the MOC of the survey (tick coverage
\includegraphics[width=0.1\textwidth]{../images/aladin_load_coverage.png}). For
the moment make the two MOC planes invisible by clicking on their opacity slider
\includegraphics[width=0.04\textwidth]{../images/aladin_button_opacity.png}.
\begin{figure}[H]
\center
\includegraphics[width=0.7
\textwidth]{../images/aladin_load_sdss-image-moc.png}
\caption{Selecting the SDSS 9 coloured survey and MOC}
\label{fig:aladinselect}
\end{figure}

    \item Turn on the coordinate \textbf{grid}
\includegraphics[width=0.035\textwidth]{../images/aladin_button_grid.png}, zoom
out and use
the \textbf{pan} tool
\includegraphics[width=0.035\textwidth]{../images/aladin_button_pan.png} to
explore the whole sky.

    \item Now turn the MOC planes back on (click again on the opacity slider).
Zoom onto the edges of the surveys and note the way the MOC represents the
coverage of the surveys.

    \item Calculate the intersection of the coverage maps of the SDSS and
GALEX surveys using in the menu the item \textbf{Coverage $\rightarrow$
Logical operations} or the MOC button
\includegraphics[width=0.035\textwidth]{../images/aladin_button_moc.png} on the
right of the main viewing window.

\begin{figure}[H]
\center
\includegraphics[width=0.4 \textwidth]{../images/aladin_moc_intersection.png}
\caption{Building the intersection of the coverage maps}
\label{fig:intersec}
\end{figure}

    \item Load the full Webb 1996 Arp catalogue that you saved earlier. You
can do this in one of the following three ways:
    \begin{itemize}
        \item \textbf{File $\rightarrow$ Load local file... }.
        \item Drag and drop on the stack.
        \item Broadcast the catalogue from the \vizier\ page that shows the
        HTML version of the table or \textbf{MyData} area of the CDS Portal. To
        do so click on \includegraphics[width=0.035\textwidth]
        {../images/vizier_button_broadcast.png}
        or \includegraphics[width=0.035\textwidth]
        {../images/cdsportal_button_broadcast.png} respectively and allow the
        browser to connect to the SAMP hub. For \vizier\ you additionally have
        to click on the newly appeared grey \textbf{Broadcast} button and in
        your \textbf{MyData} area of the CDS Portal you might have to click the
        same broadcast button again after granting your browser permission to
        connect to the SAMP hub. Now the data appears in \aladin.
    \end{itemize}
Alternatively you can download the catalogue from \vizier\ through the
\textsc{Data Tree}, enter "Arp Webb" in the \textbf{Select} line below the
\textsc{Data Tree}, select the "arplist" table and \textbf{Load} the
\textbf{Whole data}.

    \item Filter the catalogue to select only the sources that fall within
the SDSS+GALEX MOC: \textbf{Coverage $\rightarrow$ Filter a table by
MOC...}: a new catalogue plane appears and the filtered catalogue contains 425
sources. You can find the number for example in the
little information text that appears on the top of the stack when hovering the
mouse over an entry in the stack. Note that you can also filter a table by MOC
\includegraphics[width=0.09\textwidth]{../images/aladin_load_byMOC.png}
when loading the table initially (instead of loading the entire table).
\begin{figure}[H]
\center
\includegraphics[width=0.4
\textwidth]{../images/aladin_moc_filter-tab-by-moc.png}
\caption{Filtering a catalogue by a MOC}
\label{fig:filtermoc}
\end{figure}

    \item Visualize the brightest ($<$9~mag) galaxies of the selected
sources by extracting small images from the SDSS survey:

    \begin{itemize}
        \item Select the brightest galaxies using the \textbf{filter} tool
        \includegraphics[width=0.04\textwidth]
        {../images/aladin_button_filter.png}: select the
        \textbf{Show brightest stars} predefined filter and edit it with the
        \textbf{Advanced mode} to select object with magnitude below 9. Note
        that the column is automatically identified with the Unified Content
        Descriptor `~phot.mag* '.
        \item Make sure that only the MOC filtered catalogue is active in the
        stack and visible in the main viewing window (or other sources may also
        be filtered). An easy way to ensure that is to delete every catalogue
        not useful any more.
        \item Click on \textbf{Apply} and then \textbf{Export} to create a new
        plane consisting only of sources selected by the filter. There are 7
        sources with magnitudes below 9.
    \end{itemize}
\begin{figure}[H]
\center
\includegraphics[width=0.4 \textwidth]{../images/aladin_filter_mag.png}
\caption{Filtering a catalogue by magnitude}
\label{fig:filtermag}
\end{figure}
\item Make thumbnails of the selected brightest sources: \textbf{Tool
$\rightarrow$ Thumbnail view generator...}, set the thumbnail size to
14\,arcmin.
\begin{figure}[H]
\center
\includegraphics[width=0.6\textwidth]{../images/aladin_thumbnails.png}
\caption{Thumbnails}
\label{fig:thumbnails}
\end{figure}
\end{itemize}
This time we keep some of the planes that we created. In particular, please do
not clean away the table of the seven brightest galaxies.

\section{Automation [Optional]}
When samples become larger, it is useful to automate some tasks. In this
optional section we will explore how to execute some tasks with
scripts.

\subsection{Collect information on a sample of galaxies using \aladin}

Use an \aladin\ script to obtain DSS and SDSS image with HST, Chandra, ESO
observation log overlays for each of the selected bright galaxies.
\renewcommand\UrlFont{\color{blue}\rmfamily}
\begin{itemize}
    \item Copy the script Arp\_script.ajs from the url \\
    \url{http://cds.unistra.fr/tutorials/CDS-tutorial/Arp_script.ajs} \\
     to your computer or create a new file with the script shown at the end
    of this section.
    \item Create a folder called `Arp' and edit the script Arp\_script.ajs to
    insert a path in order to save the output files, e.g. $\sim$/Desktop/Arp.
    \item Open the \aladin\ macro controller and load the script:\\
    - \textbf{Tool $\rightarrow$ Macro Controller} then \textbf{File
    $\rightarrow$ Load script}\\
    - or cut and paste the script into the top panel of the \textsc{Macros}
    window.
    \item Select the table with the seven brightest sources from the peculiar
    galaxy catalogue:\\
    - Right click on the plane and \textbf{Select all objects in the selected
    planes}\\
    - In the \textsc{Macros} window: \textbf{File $\rightarrow$ Use selected
    plane sources as params}.\\
    - Note how the catalogue columns are shown as parameters which can be
    referred to as \$1, \$2, etc within the script.
    \item Click on the first row of the parameters table and execute the script
    for this row: \textbf{Exec current params}.
    \item Optional: add an SDSS image: remove the `\#' to enable download of a
    SDSS g-band image for each source. Note that this results in an
    \textbf{Could not find any data corresponding to your request} message for
    objects not covered by SDSS.
    \item Inspect the output in the \aladin\ window and also the files written
    in the Arp folder.
    \item Execute the script for all sources: \textbf{Exec all from current}.
    \item Note that the saved stack files ($\ast$\_stack.aj) can simply be dragged and dropped
    into \aladin\ for inspection.
\end{itemize}
This is the script:
\begin{verbatim}
#AJS
#
reset
grid on

# DSS image:
"ARP-$2_DSS" = get DSS.STScI(POSS2UKSTU_Red,15,15) $3

# SDSS image:
# "ARP-$2_SDSS" = get SDSS(keyword=Filter g) $3

# SIMBAD plane
# "ARP-$2_Simbad" = get Simbad $3 5'

# Observation Logs
viz_logHST=get vizier(logHST) $3
viz_logESO=get vizier(logESO) $3
viz_logChandra=get vizier(logChandra) $3

sync
pause 1

# Write results to files
# export B/hst/hstlog /Path/To/Datafolder/Arp/Arp-$2_HST.xml
save /Path/To/Datafolder/Arp/Arp-$2_chart.png
backup /Path/To/Datafolder/Arp/Arp-$2_stack.aj
#adapt ^^^^^^^^^^^^^^^^^^^ to your own path
\end{verbatim}
\begin{figure}[H]
    \center
    \includegraphics[width=0.38 \textwidth]
    {../images/aladin_macrocontroller_cdstutorial.jpg}
    \caption{\textsc{Macros} window \& Arp\_script.ajs }
    \label{fig:script}
\end{figure}



\subsection{Visualise the distribution of Arp's galaxies on the Sky}
The scripting language Python is becoming more and more widely used by
Astronomers. Consequently, more and more Virtual Observatory services are
available through Python. To explore some of the features that Python can
provide today, a Jupyter notebook was prepared. These notebooks allow
interactive execution of Python code. Go now to\\
\url{https://mybinder.org/v2/gh/cds-astro/tutorials/master?filepath=Notebooks}\\
and wait a moment for everything to load. Click on the link to

\textbf{The\_CDS\_tutorial.ipynb} or \textbf{The\_CDS\_tutorial\_extended.ipynb}

\noindent and follow the instructions there. You can also download the Jupyter
notebook from github repository to your machine. It was created to run with the
packages as listed in the requirements.txt file. Using
pip\footnote{\url{https://pip.pypa.io/en/stable/}} or
conda\footnote{\url{https://docs.conda.io/en/latest/}} you can install all
these packages.

\end{document}