Tabbed layout for Xamin results added to Xamin version 5.0

Xamin version 5.0 introduces the tabbed layout for grid formatted query results. This new output format replaces the current multi-window grid output. All new queries will be added to one main panel and each can be displayed by clicking its associated tab (figure 1). Tabs are labeled with the query number and mousing over the tab will display the more descriptive table name. Grids can be separated from the panel with a drag gesture, typically by clicking on the associated tab and dragging it to the desktop (figure 2). Tabs cannot be dragged back to the main panel.

figure 1

figure 2

Query visualization introduced with Xamin version 5.0

An interactive visualization component using the AladinLite data visualizer developed at the Centre de Données astronomiques de Strasbourg (CDS) has been added to Xamin grid queries. This new feature allows users to select regions visually and to display the location of observations and targets against images of the HEASARC archive holding. User can also select an area within the Aladin widow to transfer coordinates to the Xamin window for a new query.

Positional grid-formatted queries will trigger the associated region and query results to be displayed in the Aliadin Lite window (figure 1). Results will be  shown as markers on the image.

Selecting a row in the results grid highlights the element in the Aladin window and vice-versa. (1, 2). Users can immediately determine the identity of interesting objects, or pick out objects with special non-spatial characteristics. The bar below the image window (3) shows the title of the associated grid. Clicking the Aladin icon (4) on the desktop will redisplay the Aladin window and bring it to the forefront. Clicking the Update icon (5) will replace the markers in the Aladin window with currently displayed query results. Clicking the Restore icon (6) will return the Aladin window to the initial state of the displayed query results.

Different background image data can be selected from a list of missions (figure 2).

A shift-click in the Aladin window (figure 3) will encircle the clicked position (1) and transfer the center coordinates and radius of the enclosed circle to the Xamin window (2) in quick preparation for a new query.

figure 1

AladinLite Window displayed in Xamin showing image base layer selections

figure 2

figure 3

The State of Xamin and Browse

You may have noticed that a few problems have plagued the Browse and Xamin services over the last week. We have resolved many issues but anticipate that a few may still be pop up. We appreciate your patience as we implement this government mandated transition from http to https. Feel free to contact us if you have problems via the Browse Feedback form or Bug reports and Feature requests page under the Xamin Help menu.

Xamin Batch Interface issues

A new version of the jar file used for the Xamin command line interface has been released. The older version contains a URL that is no longer valid and queries using this jar file will fail.

There are two ways to fix this:

  • Users can download a new version of Xamin’s users.jar file
  • Users can use the existing users.jar but need to specify the environment variable XAMIN_CLI_URL to point to https://heasarc.gsfc.nasa.gov/xamin/cli

If you have questions please let us know. We apologize for the inconvenience.

Xamin update August 2016

For this Xamin update we have reinstated the Product Explorer for Grid queries and added bibliography table options.

  • The Product Explorer allows users to see and select the kinds of products associated with query results displayed as a grid. Look for the Product Explorer button in the top toolbar of grid table results. Documentation can be found on our Xamin Web Guide
  • Xamin now accepts two new arguments at run time:

       bibbase=xxx

    can be used to point to a table you want to use as your base zzbib table. In principle this can be a user table (but you need to log in separately).

       bibext=xxx

    can be used to point to a table you want to use to supplement the zzbib table. I.e., if you want to use mybib as your base bibliography table use

    http://heasarc.gsfc.nasa.gov/xamin?bibbase=mybib

    This assumes (but does not check) that a table mybib exists.

Xamin Version 3.0

Yesterday we released a major update to our Xamin interface. We hope the new interface is more attractive and user friendly. It also includes a major upgrade to the underlying JavaScript library. Features in the new interface are described below. If you want to get back to the old style, that interface is still around. You can get back to it using the links provided, or you can start using the URL http://heasarc.gsfc.nasa.gov/xamin/xamin_old.jsp

Release notes for the new version:

  • The Application Console:
    The overall look for the Xamin Web interface is very different. It emulates a computer console. If you expand your browser to use the full screen the console emulation can be quite close. There are buttons along the bottom of the interface that allow you to display and hide each major pane active in your Xamin session. Buttons in the background can be used to activate the query, feedback, information and user panes.
  • Start Button:
    The ‘Start’ — named for its location more than its functionality — button (bottom left) allows users to get to standard windows, to change the background and to organize, hide, or delete all data windows.
  • Session configuration:
    The Session menu in the Query pane now has a submenu allowing you to set up a saved session configuration that will be automatically applied when you start an Xamin session. This uses a persistent cookie so that it does not require a user account. However since the amount of information that can be stored in the cookie is small, it is mostly useful for storing default menu configurations and the like. Adding a table may exceed the capacity of the cookie and the attempt to save the configuration will fail.
  • Output formats:
    In the Options menu in the Query Pane users now have many more output format options including text downloads and rendering text in other windows.
  • Theme option removed:
    There were three somewhat different themes allowed in the old version. These changed the color scheme (and sometimes scaling) of the display but had no other effect on functionality.
  • Options:
    The Options menu has been reorganized a bit to try to put things together more logically in the sub menus. E.g., the Output content submenu now controls the coordinate and time formats, whether data are rounded and which fields are shown by default.
  • Query start buttons:
    The buttons used to start queries have been simplified a bit. Instead of two buttons used to start index queries where we look for tables which have data matching your criteria, there is now a single button whose label text indicates if the query will be made for all HEASARC tables or look only within the set of tables you have specified.
  • Index and table query buttons switched:
    The relative positions of the index and table query buttons have been reversed. The table query buttons now come first.Similarly, there are now only three buttons to submit queries of tables. You use the same button to start a single table query or a correlation. You pick the button based upon whether you wish to see the results as a table, do a plot or save the results in your Xamin environment.
  • Bibcodes:
    Users can now explicitly enter bibcodes for discovery and table queries.
  • File uploads:
    You can immediately upload a file to use in queries in Xamin without having to first log in to a user account. The file can be used in a sequence of queries, but it will be uploaded each time. [We originally made this change in the development version, but moved it into the operational system early.]
  • Virtual Observatory Tables:
    Many more virtual observatory resources are available.
  • Keyword search results:
    The results for a keyword search of tables are now formatted where you can collapse and expand the results for HEASARC and VizieR to focus on the tables you are interested in. More information about VO table resources is now available through the information panel.
  • Keyword search results queries:
    You can now choose to add the list of HEASARC tables matching your keyword search into the selected tables. You can then do a search (typically an index query since you cannot do correlations on more than 4 tables) on those tables. Xamin V2 also had facilities to search these tables in an index query but did so using an inefficient query syntax. Results will now return much faster.
  • Selecting parameters:
    The parameter explorer has been substantially revised. Previously a red parameter bar was used to signal the end of the displayed parameters. Users could drag this bar to change what parameters were to be displayed, or move parameters around. It is still possible to move parameters (including groups of parameters) around, but there are now icons on each parameter to select/deselect the parameter. Each row also an icon for changing the boundary between the selected/deselected parameters
  • Printouts:
    The ability to print queries has been improved and expanded. Discovery queries (where a list of tables containing matching objects is retrieved) and plots can now also be printed. Any pane that can be printed has a printer tool on the right of the title bar.
  • Feedback:
    The same form is now used to both submit new feedback requests and display existing feedback.
  • No prompt on exit:
    Xamin no longer prompts for confirmation that you want to leave the service when you have more than one plot/table displayed.
  • Multiple plot control windows:
    Previously only a single plot control window was allowed. When a new plot request was made any existing plot control window was destroyed and replaced by the result from the new plot request. Since these are bulky windows, users may want to remove them as soon as they are finished with a particular plot. Plot control windows are cleaned up when users use the Clear Data option on the Start button.
  • Single box notice:
    When using the single box interfaces users will be notified immediately when the single box query initiates. Previously the system could appear inactive while Xamin was checking whether input parameters were target names.
  • Tutorial movies:
    The introductory tutorial in the Xamin Web Users Guide is now given as a set of movies rather than text.  We also have a Introduction to Xamin page.

Enhanced Bibcode Access In Xamin

The recently released version 2.1.6 of Xamin has some enhanced capabilities for handling bibcode queries. For some time the web interface has allowed users to ask whether any tables have rows that index observations which are referenced in a particular article using the syntax

http://heasarc.gsfc.nasa.gov/xamin/xamin.jsp?bibcode=xxxx

where xxxx is the 19 character bibcode. The new version gives a bit more feedback about which bibcode was used when such queries are made.

The zzbib table can be used to find tables and rows matching a particular bibcode in the batch interface with a syntax like

java -jar users.jar table=zzbib constraint=bibcode="'xxxx'"

E.g.,
java -jar users.jar table=zzbib constraint=bibcode="'2014Natur.505..378C'"
bibcode |table_name|id_fields|id
2014Natur.505..378C|rosmaster |seq_id |RP200984N00
2014Natur.505..378C|rosmaster |seq_id |RP201583N00
2014Natur.505..378C|rosmaster |seq_id |RP201584N00
2014Natur.505..378C|rosmaster |seq_id |RP201585N00
2014Natur.505..378C|rosmaster |seq_id |RP201586N00
2014Natur.505..378C|rosmaster |seq_id |RP201587N00

Number of rows: 6
Number of columns: 4

will find the rows in zzbib that reference a particular bibcode. The other fields in zzbib indicate the table, the column of the table used to id specific rows the table, and the value for that id. [Note that since the bibcode is a string parameter in the zzbib table, the bibcode must be enclosed in single quotes. The enclosing double quotes make sure that the single quotes are actually part of the parameter and not processed by the shell.]

In the new release of Xamin you can also add bibcode constraints to particular tables with the new bibcode parameter:

java -jar users.jar table=rosmaster bibcode=xxxx

We can repeat our example above but get the actual data for the ROSMASTER rows

java -jar users.jar table=rosmaster bibcode=2014Natur.505..378C
seq_id |instrument|exposure|ra |dec |name
RP201587N00|PSPCB | 7749|22 43 33.6|44 00 00|EV LAC
RP201586N00|PSPCB | 5928|22 43 07.2|44 10 12|EV LAC
RP201585N00|PSPCB | 4561|22 43 09.6|44 10 12|EV LAC
RP201584N00|PSPCB | 3854|22 43 07.2|44 12 36|EV LAC
RP201583N00|PSPCB | 3445|22 43 07.2|44 13 12|EV LAC
RP200984N00|PSPCB | 2673|22 46 50.4|44 19 48|GL 873

Number of rows: 6
Number of columns: 6


will find all the rows in rosmaster referred to in a particular bibcode. You can add additional constraints to the query if you like. In this context since we have special processing of the bibcode it need note be enclosed in quotes, but if the bibcode contains special characters like ampersand you may need to use quotes or some other mechanism to escape shell processing.

The Xamin Command Line Interface (CLI) and Data Products

We recently reviewed how data products are handled in the Xamin Command Line Interface and feel that some information on how to download data products might be helpful. (For help getting set up to use the CLI interface see our documentation.)

Let’s start with an example. The following command will return table results from the suzamaster table for object cen a:

java -jar users.jar table=suzamaster position="cen a" fields=name,ra,dec

The output is:

name |ra |dec |exposure
Cen A |13 25 28.68|-43 01 03.7|64675.90000
CENTAURUS_A|13 25 21.86|-43 04 19.2|62432.80000
CENTAURUS_A|13 25 19.73|-43 04 07.7|51278.70000
CENTAURUS_A|13 25 18.74|-43 03 53.6|55944.20000
CENTAURUS A|13 25 27.60|-43 01 09.0| -99.00000
CENTAURUS A|13 25 27.60|-43 01 09.0| -99.00000
Number of rows: 6
Number of columns: 4
—- Messages —-
Info: Search Radius
Search radius: 10′ from suzamaster

Info: Name resolution
Position cen a corresponds to J2000 decimal coordinates:201.365063 -43.019112
—————–

If you want to list the data products for each row add the parameter “products” to the command:

java -jar users.jar table=suzamaster position=”cen a” fields=name,ra,dec products

The output for this command is:

name |ra |dec |exposure
Cen A |13 25 28.68|-43 01 03.7|64675.90000

# Product suzaku.obs: Observation Directory
> /FTP/suzaku/data/obs/1/100005010/

# Product link.suzaxislog: Suzaku XIS Configuration Log
> query?table=suzaxislog&constraint=obsid=100005010

CENTAURUS_A|13 25 21.86|-43 04 19.2|62432.80000

# Product suzaku.obs: Observation Directory
> /FTP/suzaku/data/obs/7/704018010/

# Product link.suzaxislog: Suzaku XIS Configuration Log
> query?table=suzaxislog&constraint=obsid=704018010

CENTAURUS_A|13 25 19.73|-43 04 07.7|51278.70000

# Product suzaku.obs: Observation Directory
> /FTP/suzaku/data/obs/7/704018020/

# Product link.suzaxislog: Suzaku XIS Configuration Log
> query?table=suzaxislog&constraint=obsid=704018020

CENTAURUS_A|13 25 18.74|-43 03 53.6|55944.20000

# Product suzaku.obs: Observation Directory
> /FTP/suzaku/data/obs/7/704018030/

# Product link.suzaxislog: Suzaku XIS Configuration Log
> query?table=suzaxislog&constraint=obsid=704018030

CENTAURUS A|13 25 27.60|-43 01 09.0| -99.00000
CENTAURUS A|13 25 27.60|-43 01 09.0| -99.00000

Number of rows: 6
Number of columns: 8

—- Messages —-
Info: Search Radius
Search radius: 10′ from suzamaster

Info: Name resolution
Position cen a corresponds to J2000 decimal coordinates:201.365063 -43.019112
—————–

As you can see, if data products are available then product names and partial URLs strings are listed below each row of the table results. These URL strings can used with a command line data transfer tool (eg. wget, curl) to download data from the HEASARC server.

In this example there are two types of URLs – one type is used to download data products (eg., > /FTP/suzaku/data/obs/7/704018030/) and the other type (eg., > query?table=suzaxislog&constraint=obsid=100005010) is used to display data from related tables.

For data product downloads an example of a wget command for Unix type machines would be:

wget -q -nH -r -l0 -c -N -np -R ‘index*’ -erobots=off –-retr-symlinks –cut-dirs=1 http://heasarc.gsfc.nasa.gov/FTP/suzaku/data/obs/1//100005010/

If you are interested in what each of the wget options does take a look at this recent blog post.

If you would like to download data products at the same time that you run the java command the following Unix shell script example should work:

#!/bin/sh
java -jar users.jar table=swiftxrlog position=ngc4626 products | \
grep '>' | \
sort | \
uniq | \
sed -e "s/ > \/FTP/wget -q -nH --cut-dirs=6 -r -l0 -c -N -np -R 'index*' -erobots=off --retr-symlinks http\:\/\/heasarc.gsfc.nasa.gov\/FTP/" | \
sh

The URL string for Link Products (e.g., link.suzaxislog) can be used to view Xamin catalog results for related tables. An example of this type of command is:

wget -O suzaxislog_results “http://heasarc.gsfc.nasa.gov/xamin/query?table=ascamaster&radius=60&position=22+02+43.2,42+16+48″

The output is a list of rows from the ascamaster table for object cen a.

We will be creating a post soon with download instructions for users who may not have access to all the commands (eg, sed) used in our example shell script.

Xamin Data Products Download Commands

In addition to the option to download data products as a tar file Xamin will display a list of separate download commands. Users can then transfer individual data files from the command line or create a download script.

These download commands are listed under the Wget Commands Tab of the Products Cart as seen in this screen grab:

wgetcommands

wget is a very useful command with many, many options and it took some time to determine which options were needed to traverse the complicated HEASARC data products directory structure to find and transfer the products.

The following is one of the wget commands listed in the Products Cart.

wget -q -nH -r -l0 -c -N -np -R 'index*' -erobots=off --retr-symlinks --cut-dirs=7 http://heasarc.gsfc.nasa.gov/FTP/chandra/data/science/ao01/cat5//1828/primary/acisf01828_001N004_fov1.fits.gz

We thought some of our users might be interested in knowing exactly what these options do. We used GNU Wget online manual for most of our research.

-q: quiet mode, no output is displayed

-nH: directories created on the user’s system will not be named using the HEASARC host name

-r -10: directories will be searched recursively up to 10 levels down

-c: files only partially downloaded from a previous execution will continue to to downloaded

-N: a file will not be downloaded if a local file of the same name exists and is newer

-np: the search will not ascend up to the parent directory during recursion

-R ‘index*’: unnecessary files will not be downloaded

-erobots=off: do not observe directives from the robots.text file that might prevent downloads

–retr-symlinks: symbolic links are traversed and the pointed-to files are retrieved

–cut-dirs=N: skip N number of the components in the URL directory structure when the directory structure is created on user’s system

Xamin V2.2 Released

The major change to this version is that Xamin now generates preview image windows giving SkyView survey cutouts for queries that involve a single position. By default DSS and RASS cutouts are created, but this can be controlled in the Options/Query Control/Survey Img. option. The cutouts start out as 100×100 but can be resized and the image will be appropriately recomputed.

The internal release procedures have also been significantly updated but this will not affect users.