***SkyView* in a Jar**

**Using SkyView as a Standalone Java Application**

*Thomas McGlynn and Laura McDonald*

High Energy Astrophysics Science Archive Research Center

Goddard Space Flight Center

Greenbelt, MD 20771

Version 1.91

March 1, 2006

**Table of Contents**

[1. Introduction 3](#introduction)

[2. Setup. 3](#setup.)

[3. SkyView-in-a-Jar and ImageJ 4](#skyview-in-a-jar-and-imagej)

[4. Command Summary 4](#command-summary)

[4.1 Default arguments 12](#__RefHeading___Toc128713241)

[5. Example requests. 13](#example-requests.)

[6. The Cache 14](#the-cache)

[6.1 Caching the Digitized Sky Survey.
15](#caching-the-digitized-sky-survey.)

[7. Dependencies on Remote Systems 15](#dependencies-on-remote-systems)

[8. Compatibility with the SkyView Batch Interface
16](#compatibility-with-the-skyview-batch-interface)

[9. SkyView-in-a-Jar Operations. 16](#skyview-in-a-jar-operations.)

[9.1 Getting defaults and user arguments.
17](#getting-defaults-and-user-arguments.)

[9.2 Updating Settings. 17](#updating-settings.)

[9,3 Locating surveys. 17](#locating-surveys.)

[9.4 Looping over the surveys. 18](#looping-over-the-surveys.)

[9.5 Getting candidate survey images
18](#getting-candidate-survey-images)

[9.6 Building images. 18](#building-images.)

[9.7 Finding the best survey image for each output pixel.
19](#finding-the-best-survey-image-for-each-output-pixel.)

[9.8 Preprocessing 20](#preprocessing)

[9.9 Validating the image. 20](#validating-the-image.)

[9.10 Resampling setup. 20](#resampling-setup.)

[9.11 Sampling in energy. 21](#sampling-in-energy.)

[9.12 Sampling in space. 21](#sampling-in-space.)

[9.13 Post-Processing 21](#post-processing)

[9.13.1 De-edging 21](#de-edging)

[9.13.2 Graphics Processing 22](#graphics-processing)

[9.14 Data conversion and writing the FITS file.
22](#data-conversion-and-writing-the-fits-file.)

[9.15 Cache cleanup. 22](#cache-cleanup.)

[10. Survey Definition File 23](#survey-definition-file)

[Survey 23](#survey)

[10.1 ShortName 23](#shortname)

[10.2 Name 23](#name)

[10,3 Description 23](#description)

[10.4 Settings 24](#settings)

[10.5 MetaTable 24](#metatable)

[10.6 OnlineText 25](#onlinetext)

[10.7 FITS 25](#fits)

[11. The \< Images\> Element 26](#the-images-element)

[11.1 Explicit Image Lists 26](#explicit-image-lists)

[11.2 Image Generators 27](#image-generators)

[11.3 Example \<Images\> elements 28](#example-images-elements)

[12. A Simple Survey Definition File
29](#a-simple-survey-definition-file)

[13. Contents of the JAR file 29](#contents-of-the-jar-file)

[13.1 The Class Files 29](#the-class-files)

[13.2 Survey Data and Metadata 30](#survey-data-and-metadata)

[13.3 Control Files 30](#control-files)

[13.4 Source code 30](#source-code)

## 1. Introduction

*SkyView*-in-a-Jar provides users with a local *SkyView* system on their
own machines. Users can generate FITS, GIF, JPEG, ... images from major
surveys in any requested geometry, resample and mosaic their own data
and create their own surveys. *SkyView*-in-a-Jar comes completely ready
to use as a single file. In this default configuration almost all
surveys accessible through the *SkyView* web pages are available. It is
easy to add new surveys using local files or the Virtual Observatory
Simple Image Access protocol.

The code itself is also extremely extensible. Users can add new
samplers, projections, and coordinate systems. Even the classes which
define the basic algorithms for finding surveys, selecting images within
the survey, and mosaicking the images can be overridden by the
sophisticated user. Users can insert their own pre- and post- processing
functions to modify the input data or the resulting image.

This document provides a comprehensive User's Guide to
*SkyView*-in-a-Jar.

## 2. Setup.

*SkyView*-in-a-Jar is self-contained within a single executable JAR
file. JAR files are a modified version of ZIP files used to store Java
code. However JAR's can include data and program control files as well
as the Java code. *SkyView*-in-a-Jar contains all of the control files
needed to access the surveys available from *SkyView*'s standard Web
interface. For a few surveys the survey data itself is included. For
these surveys not even network connections are required. The other
surveys are accessed through standard Web protocols.

Users can download the JAR file from

http://skyview.gsfc.nasa.gov/jar/skyview.jar

and then run the file using the command

java --jar skyview.jar key1=arg1 key2=arg2 ...

The same JAR file is used for all operating systems. This program
requires at least a Java 1.5 (sometimes called Java 5.0) environment to
run. Java distributions for most major operating systems are available
at

> http://www.java.sun.com.

E.g., to create a DSS and FIRST images of 3c273 simply enter

java --jar skyview.jar survey=DSS,FIRST position=3c273

The program creates output1.fits and output2.fits. The first contains an
image resampled from the DSS and the second contains data from FIRST.

There are many options controlling how to generate and resample the
image. These are discussed briefly in the command summary section and
then in more detail in the context of how *SkyView* works.

The *SkyView* Java classes in the JAR file can be used in other
applications as well. Simply include the JAR file in your CLASSPATH. The
only difference between a regular and executable JAR file is that the
later contains a manifest that indicates how to start up when the --jar
option is used in the java command. The *SkyView* Java application could
also be started up with

> java --cp pathto/skyview.jar skyview.executive.Imager key1=arg1 ...

The Imager class could be instantiated within other Java applications as
well as being invoked from the command line.

Later versions of the JAR files may start a different class, but this
method of using the Imager class should still work, and the command line
arguments will be upwardly compatible.

## 3. SkyView-in-a-Jar and ImageJ

Starting with version 1.9, the *SkyView* JAR also contains a complete
distribution of the ImageJ image display and analysis tool. ImageJ is a
very powerful public domain software package developed by Wayne Rasband
<(wsr@nih.gov)> at the National Institutes of Health. *SkyView*
currently uses ImageJ functions for creating quicklook images in GIF,
JPEG and other formats, including various scaling and color table
operations. ImageJ has many other capabilities for users may to analyze
images created by *SkyView.* Hundreds of plug-in modules are also
available that provide powerful functionality in diverse areas.

Users should be able to start ImageJ itself with the *SkyView* JAR using
the command

java --cp skyview.jar ij.ImageJ \[other arguments\]

or they can download the ImageJ JAR file at
<http://rsb.info.nih.info/ij>. Much more information on ImageJ is
available at that site. Future versions of the *SkyView* are likely to
use additional ImageJ functionality. The *SkyView* JAR includes both the
ImageJ

class and source code. Note however that the class files are copied
directly from the ImageJ distribution version v1.35r and have not been
recompiled from the source.

## 4. Command Summary

This section describes the command line arguments to the
*SkyView*-in-a-Jar application. Each command line argument consists of a
*key=value* pair. The command keys are case-insensitive. In some cases,
particularly when the value is a file or class name, the values may be
case-sensitive. Generally, to associate more than one value with a key,
the values are separated by commas.

+-------------+--------------------------------------------------------+
| **SkyVi     |                                                        |
| ew-in-a-Jar |                                                        |
| Command     |                                                        |
| Line        |                                                        |
| Arguments** |                                                        |
+-------------+--------------------------------------------------------+
| **Key**     | **Value**                                              |
+-------------+--------------------------------------------------------+
| Survey      | The survey or surveys indicate which surveys the user  |
|             | wishes to generate an image for. If more than one      |
|             | survey is desired, the values should be separated by   |
|             | commas. The list of all surveys known (by default) to  |
|             | the program can be generated by invoking the           |
|             | application with no arguments. This will give a quick  |
|             | description of the arguments and a list of known       |
|             | surveys. Survey names are case insensitive.            |
|             |                                                        |
|             | The survey user is special. It indicates that one or   |
|             | more files indicated in the userfile argument are to   |
|             | be used as the survey. Using the survey=user and       |
|             | userfile=file1,file2,... arguments, users can resample |
|             | and mosaic local data files.                           |
|             |                                                        |
|             | Survey=DSS,2MASS-K                                     |
+-------------+--------------------------------------------------------+
| **Output    |                                                        |
| image       |                                                        |
| geometry**  |                                                        |
+-------------+--------------------------------------------------------+
| Position    | The position argument gives the center position for    |
|             | which images are requested. It may be either a         |
|             | coordinate pair, or a target name. The position        |
|             | argument or the Lon/Lat pair is required.              |
|             |                                                        |
|             | Position=3c273                                         |
|             |                                                        |
|             | Position='10 20 30, -15 16 22'                         |
|             |                                                        |
|             | Note that the quotes are not part of the actual value: |
|             | they are needed to ensure that the value is treated as |
|             | a single string. Your operating system may have other  |
|             | methods for enclosing embedded spaces in an argument.  |
+-------------+--------------------------------------------------------+
| Lon         | This argument gives the Longitude or right ascension   |
|             | of the center of the image. Lon/Lat arguments          |
|             | supersede the position if both are specified.          |
+-------------+--------------------------------------------------------+
| Lat         | This argument gives the Latitude or declination of the |
|             | center of the image.                                   |
+-------------+--------------------------------------------------------+
| Coordinates | This argument gives the coordinate system used for the |
|             | output image. The first letter in the value gives the  |
|             | type of coordinates. If a number is appended then this |
|             | is the epoch of the equinox of the coordinate system.  |
|             |                                                        |
|             | Recognized values include                              |
|             |                                                        |
|             | J \-- Julian equatorial coordinates                    |
|             |                                                        |
|             | B \-- Besselian equatorial coordinates                 |
|             |                                                        |
|             | ICRS -- International Coordinate Reference System      |
|             | coordinates.                                           |
|             |                                                        |
|             | Gal -- Galactic coordinates                            |
|             |                                                        |
|             | H -- Helioecliptic coordinates                         |
|             |                                                        |
|             | E \-- Ecliptic coordinates.                            |
|             |                                                        |
|             | The single letter values may be combined with an       |
|             | epoch, e.g.,                                           |
|             |                                                        |
|             | J2000, B1950, E2020.123                                |
|             |                                                        |
|             | The default coordinate system is J2000.                |
|             |                                                        |
|             | Coordinates=J2000                                      |
|             |                                                        |
|             | Coordinates=Galactic                                   |
+-------------+--------------------------------------------------------+
| Projection  | The three letter designation used to specify the       |
|             | projection of the output image. This uses the suffix   |
|             | in the FITS CTYPE keywords. Supported projections      |
|             | include Car, Tan, Ait, Zea, Sin and Csc.               |
|             |                                                        |
|             | The default is Tan.                                    |
|             |                                                        |
|             | Projection=Tan                                         |
+-------------+--------------------------------------------------------+
| Equinox     | If the coordinate system only specified a coordinate   |
|             | type, the equinox can be specified separately.         |
|             |                                                        |
|             | Equinox=1980                                           |
+-------------+--------------------------------------------------------+
| Scale       | Scale gives the size of pixels in the output image and |
|             | corresponds to the CDELT keywords. Scale may be        |
|             | specified as a scalar, in which case the pixels are    |
|             | square, or two values may be given if rectangular      |
|             | pixels are desired. The scale is always positive.      |
|             | Output images follow the astronomical convention where |
|             | the longitude decreases along a horizontal line. The   |
|             | scale is specified in degrees per pixel.               |
|             |                                                        |
|             | The default scale depends upon the survey. If you do   |
|             | not specify an explicit scale, and you choose more     |
|             | than one survey, then the scale may differ among       |
|             | surveys.                                               |
|             |                                                        |
|             | If there is no survey defined default, then the        |
|             | default scale is 1" per pixel. A user may specify the  |
|             | scale of individual pixels, or the size of the image   |
|             | as a whole, but not both.                              |
|             |                                                        |
|             | Scale=0.0025                                           |
|             |                                                        |
|             | Scale=0.0002777777                                     |
|             |                                                        |
|             | Scale=0.0002777777,0.0005                              |
+-------------+--------------------------------------------------------+
| Resolver    | When a target name is specified rather than specific   |
|             | coordinates, the name must be 'resolved' into          |
|             | coordinates. There are two widely used name resolvers  |
|             | available: NED and SIMBAD. The application invokes     |
|             | these through a HEASARC web service. This argument can |
|             | be used to specify which resolver or resolvers are to  |
|             | be used. If both resolvers are specified, then the     |
|             | second is checked only if the object is not found at   |
|             | the first. Values are: SIMBAD, NED, NED-SIMBAD and     |
|             | SIMBAD-NED. The default is SIMBAD-NED.                 |
|             |                                                        |
|             | Resolver=NED                                           |
+-------------+--------------------------------------------------------+
| Pixels      | This gives the number of pixels in the output image.   |
|             | If specified as a single value, the number of pixels   |
|             | will be the same in both dimensions.                   |
|             |                                                        |
|             | The default is 300.                                    |
|             |                                                        |
|             | Pixels=500                                             |
|             |                                                        |
|             | Pixels=1280,640                                        |
+-------------+--------------------------------------------------------+
| Rotation    | The argument indicates that the output image is        |
|             | rotated by the specified angle (in degrees).           |
|             |                                                        |
|             | By default there is no rotation of the image.          |
|             |                                                        |
|             | Rotation=45.0                                          |
+-------------+--------------------------------------------------------+
| **Graphic   |                                                        |
| outputs**   |                                                        |
+-------------+--------------------------------------------------------+
| Quicklook   | This argument is used to give the format for           |
|             | quicklook/graphic outputs. The supported formats are:  |
|             | GIF, JPEG (or JPG), TIFF and BMP. A value of JPG is    |
|             | assumed if there are other graphic keywords and this   |
|             | argument is not specified. The output format for three |
|             | color images (see RGB below) is always JPEG. The       |
|             | argument value is not case sensitive.                  |
|             |                                                        |
|             | Quicklook=gif                                          |
+-------------+--------------------------------------------------------+
| Scaling     | This argument controls the scaling between the data    |
|             | and the displayed images. Recognized values include    |
|             |                                                        |
|             | Linear -- The output pixels are linearly scaled from   |
|             | the input.                                             |
|             |                                                        |
|             | Sqrt \-- Output scaled as the square root of the input |
|             | pixels. Negative pixels are scaled to the minimum.     |
|             |                                                        |
|             | Log -- Output scaled logarithmically from the input.   |
|             | Negative pixels scaled to the minimum.                 |
|             |                                                        |
|             | HistEq -- Output scaled so that each output bin has    |
|             | the same number of pixels.                             |
|             |                                                        |
|             | scaling=Sqrt                                           |
+-------------+--------------------------------------------------------+
| LUT         | The argument allows the user to read in a lookup table |
|             | which will be used to translate pixels values to       |
|             | color.                                                 |
|             |                                                        |
|             | There are three sources for look up tables. ImageJ     |
|             | defines the following lookup tables internally:        |
|             |                                                        |
|             | Fire, Ice, Red, Yellow, Green, Blue, Cyan, Magenta,    |
|             | Grays, Spectrum, Red/Green, and 3-3-2 RGB.             |
|             |                                                        |
|             | There are also a set of lookup tables distributed with |
|             | the JAR file to mimic standard IDL color tables. These |
|             | may be specified using the file name                   |
|             | colortables/*xxx*.bin where *xxx* is the IDL color     |
|             | table name with spaces replaced by hyphens. (These are |
|             | also available using the syntax as the old SkyView     |
|             | Batch interface using the Batch Compatibility          |
|             | feature).                                              |
|             |                                                        |
|             | Users may also create their own color tables. The only |
|             | format currently supported is a 768 byte file          |
|             | comprising the 256 red values followed by 256 green    |
|             | and 256 blue.                                          |
|             |                                                        |
|             | When using the internally defined color tables, the    |
|             | case does not matter, but for many operating systems   |
|             | if mixed case files names are used, the argument must  |
|             | be in the correct case. Note that the program will     |
|             | always check for files with the argument in lower-case |
|             | first. If you have two LUTs xxx.lut and xXx.lut, then  |
|             | the program will always choose the former even when    |
|             | the user specifies lut=xXx.lut.                        |
|             |                                                        |
|             | If no color table is specified a gray scale image is   |
|             | produced.                                              |
|             |                                                        |
|             | lut='3-3-2 RGB'                                        |
|             |                                                        |
|             | lut=colortables/Stern-Special.bin                      |
|             |                                                        |
|             | lut=mylutDirectory/myLUT.lut                           |
+-------------+--------------------------------------------------------+
| Invert      | Invert the output. The value of this argument is       |
|             | ignored and may be elided. The output image is given   |
|             | with the color table used in inverse order (or with a  |
|             | white rather than black background if no color table   |
|             | is specified).                                         |
|             |                                                        |
|             | Invert                                                 |
+-------------+--------------------------------------------------------+
| Min         | Set the minimum value for the output image. Before     |
|             | scaling, all values below the minimum will be set to   |
|             | the minimum. This affects only the graphic image, not  |
|             | any FITS data.                                         |
|             |                                                        |
|             | min=0.                                                 |
+-------------+--------------------------------------------------------+
| Max         | Set the maximum value of the output image. Before      |
|             | scaling, all values above the maximum will be set to   |
|             | the maximum. This affects only the graphic image, not  |
|             | any FITS data.                                         |
|             |                                                        |
|             | max=256                                                |
+-------------+--------------------------------------------------------+
| RGB         | Create a color image from three surveys using the      |
|             | first as the red color, the second as green and the    |
|             | third as blue.                                         |
|             |                                                        |
|             | The output image is always created as a jpg, e.g.      |
|             | *output*\_rgb.jpg. The value of the argument is        |
|             | ignored and may be elided.                             |
|             |                                                        |
|             | RGB                                                    |
+-------------+--------------------------------------------------------+
| **R         |                                                        |
| esampling** |                                                        |
+-------------+--------------------------------------------------------+
| Ebins       | This argument is used only when sampling               |
|             | three-dimensional images which have a set of 'energy'  |
|             | values at each pixel. It must have three comma         |
|             | separated numeric values. The first gives the offset   |
|             | of the first output energy bin, the second gives the   |
|             | size of the output bins relative to the original bins, |
|             | and the third gives the number of output bins. E.g.,   |
|             | suppose we have 10 channels in the input data. We wish |
|             | to eliminate the top and bottom channels and rebin the |
|             | remaining 8 channels into 4 output bins in the output  |
|             | image. Then we have                                    |
|             |                                                        |
|             | Ebins=1,2,4                                            |
|             |                                                        |
|             | Note that the offset is 0-based. The bin size does not |
|             | need to be an integer, the output bins will be         |
|             | integrated over the input bins assuming flux to be     |
|             | uniformly distributed over the energy bin.             |
|             |                                                        |
|             | In *SkyView,* 3-D surveys normally specify a default   |
|             | for the Ebins value which gives a 2-D output image.    |
+-------------+--------------------------------------------------------+
| Sampler     | This argument specifies the sampling method to be      |
|             | used. The value consists of an algorithm designator    |
|             | which may in some cases be suffixed with an integer    |
|             | giving the order of the sampler. Currently supported   |
|             | samplers include: Nearest Neighbor (NN), Bi-linear     |
|             | interpolation (LI), Splines from 2-5 order (Spline or  |
|             | Spline3, Spline2, Spline4, Spline5), Lanczos           |
|             | interpolation with a specified kernel size             |
|             |                                                        |
|             | (Lanczos, or LanczosN where N \>= 2, the default is    |
|             | 3), and an exact-area resampling using                 |
|             | Sutherland-Hodges clipping (Clip). The default is      |
|             | nearest neighbor.                                      |
|             |                                                        |
|             | Sampler=Lanczos5                                       |
|             |                                                        |
|             | Sampler=Spline                                         |
|             |                                                        |
|             | Sampler=Clip                                           |
+-------------+--------------------------------------------------------+
| **Output    |                                                        |
| file name   |                                                        |
| and FITS    |                                                        |
| format**    |                                                        |
+-------------+--------------------------------------------------------+
| Output      | The name (or stem) of the output image or images. The  |
|             | user may specify the full path of the output image     |
|             | x.fits or just a stem x. If more than one image is     |
|             | being produced, then ordinal numbers will be added so  |
|             | that the output files will be x1.fits, x2.fits. If     |
|             | compression is requested the .gz extension should not  |
|             | be specified, it will be added automatically.          |
|             |                                                        |
|             | The default is output.                                 |
|             |                                                        |
|             | Output=\~/myoutputs/test.fits                          |
|             |                                                        |
|             | Output=c:\\datafiles\\3c273                            |
+-------------+--------------------------------------------------------+
| Compression | This flag indicates that the output files are to be    |
|             | gzip compressed. The default is not to compress the    |
|             | data. The content of the value is ignored and the      |
|             | value can be omitted.                                  |
|             |                                                        |
|             | Compression=T                                          |
|             |                                                        |
|             | Compression                                            |
+-------------+--------------------------------------------------------+
| Float       | This flag indicates the output files should be 4 byte  |
|             | reals. The default is 8 byte reals. The content of the |
|             | value is ignored and can be omitted.                   |
|             |                                                        |
|             | Float=T                                                |
|             |                                                        |
|             | Float                                                  |
+-------------+--------------------------------------------------------+
| NoFITS      | Suppress the FITS output. The value of the argument is |
|             | ignored and may be elided. This argument may be used   |
|             | in conjunction with graphics arguments if only a       |
|             | quicklook (e.g., GIF or JPEG) is desired.              |
|             |                                                        |
|             | nofits                                                 |
+-------------+--------------------------------------------------------+
| **Survey    |                                                        |
| d           |                                                        |
| efinition** |                                                        |
+-------------+--------------------------------------------------------+
| Userfile    | This argument is used to specify one or more files     |
|             | that are treated as the constituent image files of the |
|             | 'user' survey. Users can resample and mosaic local     |
|             | files easily using this argument and the user survey.  |
|             |                                                        |
|             | There is no default.                                   |
|             |                                                        |
|             | Userfile=myfile1.fits,myfile2.fits                     |
+-------------+--------------------------------------------------------+
| SurveyXML   | This argument allows the user to specify one or more   |
|             | survey XML descriptors that users can query (see below |
|             | for details of the format). Use this argument to       |
|             | specify individual files and the XmlRoot argument if   |
|             | you wish to specify an entire directory.               |
|             |                                                        |
|             | SurveyXML=surveys/mysurv1.xml,surveys/mysurv2.xml      |
+-------------+--------------------------------------------------------+
| XmlRoot     | This argument gives a directory where survey XML files |
|             | are to be found. Each '.xml' file in the directory     |
|             | will be treated as a survey descriptor file. Currently |
|             | only one directory is permitted.                       |
|             |                                                        |
|             | XMLRoot=/survey/docs/xml                               |
+-------------+--------------------------------------------------------+
| Sur         | The Survey manifest is a file (or Java resource) that  |
| veyManifest | lists survey XML files. By default the Survey Manifest |
|             | is given in the system resource                        |
|             | surveys/survey.manifest that is included in the JAR.   |
|             |                                                        |
|             | SurveyManifest=mysurvey/docs/mysurvey.manifest         |
+-------------+--------------------------------------------------------+
| **Caching   |                                                        |
| of survey   |                                                        |
| files**     |                                                        |
+-------------+--------------------------------------------------------+
| Cache       | When a survey's data is retrieved from a remote        |
|             | location, it is cached in the local file store. The    |
|             | cache argument specifies one or more directories in    |
|             | which the application should look for the remote data  |
|             | before attempting to retrieve it. If a file matching   |
|             | the desired name is found, it is used directly. The    |
|             | first directory in the cache is used to save any files |
|             | that need to be retrieved. If no cache is specified    |
|             | the current directory is used as the cache.            |
|             |                                                        |
|             | Each survey can be cached into a different directory   |
|             | by specifying a unique cache value in the Settings     |
|             | element of the Survey descriptor file or a common      |
|             | cache can be used for multiple surveys. To have the    |
|             | survey definition for the cache location have priority |
|             | over a user specified cache location, set the cache    |
|             | location in the Images area of the survey definition   |
|             | rather than in the Settings area.                      |
|             |                                                        |
|             | If no cache area is specified the current working      |
|             | directory is used.                                     |
|             |                                                        |
|             | Cache=/surveycache/cache1,/surveycache/cache2          |
+-------------+--------------------------------------------------------+
| PurgeCache  | This argument indicates that cache files are to be     |
|             | purged after the processing of that survey is          |
|             | completed. Only survey files actually downloaded in    |
|             | this request will be deleted. Other files in the cache |
|             | are left unchanged even files used in processing. The  |
|             | value of the argument is not used. All files needed    |
|             | for a given image will be downloaded before any files  |
|             | are purged.                                            |
|             |                                                        |
|             | PurgeCache=T                                           |
|             |                                                        |
|             | PurgeCache                                             |
+-------------+--------------------------------------------------------+
| **Classes   |                                                        |
| used in     |                                                        |
| p           |                                                        |
| rocessing** |                                                        |
+-------------+--------------------------------------------------------+
| S           | The class used to find surveys. This class must        |
| urveyFinder | implement the skyview.survey.SurveyFinder interface.   |
|             |                                                        |
|             | By default this is the class                           |
|             | skyview.survey.XMLSurveyFinder but it may be           |
|             | overridden by knowledgeable users.                     |
+-------------+--------------------------------------------------------+
| ImageFinder | The class used to find the which survey image to       |
|             | sample for a given output image pixel. This class must |
|             | inherit from the skyview.geometry.ImageFinder abstract |
|             | class.                                                 |
|             |                                                        |
|             | The default is                                         |
|             | skyview.geometry.imagefinder.RecursiveImageFinder      |
+-------------+--------------------------------------------------------+
| P           | One or more classes implementing the                   |
| reProcessor | skyview.geometry.Processor interface that are to be    |
|             | used in processing (presumably of the input images)    |
|             | before mosaicking takes place. If a user needs to      |
|             | communicate parameters to a pre (or post) processor,   |
|             | additional Settings can be defined which are used to   |
|             | transmit the information.                              |
|             |                                                        |
|             | No preprocessing is performed by default and no        |
|             | classes appropriate for preprocessing are currently    |
|             | provided. An input image smoother might be an          |
|             | appropriate preprocessor class.                        |
+-------------+--------------------------------------------------------+
| Mosaicker   | A class implementing the Processor interface that      |
|             | fills in the pixel values in the output image. The     |
|             | default mosaicker is the class                         |
|             | skyview.geometry.Mosaicker.                            |
+-------------+--------------------------------------------------------+
| Deedger     | A de-edger is a specific type of Post-Processor which  |
|             | allows the user to do additional processing on the     |
|             | image after it has been mosaicked.                     |
|             |                                                        |
|             | Currently the skyview.geometry.Deedger and several     |
|             | other deedging classes can be used or the user can     |
|             | write their own class.                                 |
|             |                                                        |
|             | Supplied classes are:                                  |
|             |                                                        |
|             | skyview.geometry.Deedger which de-edges using the      |
|             | default algorithm (currently using the BoundaryMedian) |
|             |                                                        |
|             | skyview.geometry.deedger.BoundaryMedian sets the       |
|             | median change across the boundary of two image to 0    |
|             |                                                        |
|             | skyview.geometry.deedger.BoundaryAverage sets the      |
|             | average change across boundaries to 0                  |
|             |                                                        |
|             | skyview.geometry.deedger.ImageMedian sets the median   |
|             | pixel value for the regions derived from different     |
|             | input images to a common value.                        |
|             |                                                        |
|             | All of these de-edgers add a constant to each of the   |
|             | images. More complex algorithms which add a slope or   |
|             | more complex flat-fielding could be coded.             |
|             |                                                        |
|             | When survey images are mosaicked together there may be |
|             | artifacts at the edges of the images where the         |
|             | different backgrounds of the images merge. The deedger |
|             | attempts to minimize these artificats. Deedging is     |
|             | turned on by default for some surveys (e.g., the DSS). |
|             | It can be turned off for those surveys with the value  |
|             | 'null' for post-processing.                            |
|             |                                                        |
|             | The de-edger is a kind of PostProcessor in many cases  |
|             | a user could use the PostProcessor setting             |
|             | equivalently. However using the Deedger setting is     |
|             | preferred since it enables and survey defaults to set  |
|             | de-edging on or off without confusion with other       |
|             | post-processors.                                       |
+-------------+--------------------------------------------------------+
| Po          | One or more classes defining the Processor interface   |
| stProcessor | which process the image after mosaicking. De-edgers    |
|             | (see above) and a graphics processor are currently     |
|             | available.                                             |
|             |                                                        |
|             | The class skyview.ij.IJProcessor handles the interface |
|             | to ImageJ functionality. A call to this processor will |
|             | normally be added whenever one of the graphic          |
|             | arguments is specified so that users do not need to    |
|             | specify this argument explicitly.                      |
+-------------+--------------------------------------------------------+
| Setti       | This argument is used to indicate classes that might   |
| ngsUpdaters | wish to look over the arguments that have been         |
|             | specified before image processing begins. E.g., one    |
|             | could build a class that translated arguments from     |
|             | French to the English values expected in the program.  |
|             |                                                        |
|             | Two classes are specified in the default settings:     |
|             | skyview.executive.BatchCompatibility and               |
|             | skyview.ij.IJProcessor. The first translates arguments |
|             | from the old *SkyView* batch interface to comparable   |
|             | values for this program. The second fills in default   |
|             | values when the user specifies some graphics keywords  |
|             | (e.g., the graphics postprocessor and the graphic      |
|             | format). Classes specified in this setting should      |
|             | implement the skyview.executive.SettingsUpdater        |
|             | interface.                                             |
|             |                                                        |
|             | SettingsUpdaters=skyvi                                 |
|             | ew.executive.BatchCompatibility,skyview.ij.IJProcessor |
+-------------+--------------------------------------------------------+

[]{#__RefHeading___Toc128713241 .anchor}**4.1 Default arguments**.

When the Java application begins, default settings are loaded. These
default settings are normally read in through the system resource
skyview.settings. If users wish to provide their own default settings,
they can override the settings provided in the JAR file by creating a
skyview.settings file in the current directory, or by pointing to a file
in any location (and of any name) using the environment variable
SKYVIEW_SETTINGS.

The settings file is a simple ASCII file. Each line can be a blank, a
comment line

(first character of the line is '#') or specify a setting. Here is what
an example file looks like:

> \# An example skyview.settings file.
>
> Pixels=500
>
> Projection=Sin
>
> Coordinates=J2000
>
> Sampler=Lanczos
>
> Equinox=2000
>
> Resolver=NED-SIMBAD
>
> XMLroot=\$SKYVIEW_XMLROOT
>
> Mosaicker=skyview.geometry.Mosaicker
>
> SurveyFinder=skyview.survey.XMLSurveyFinder
>
> ImageFinder=skyview.geometry.imagefinder.RecursiveImageFinder
>
> SettingsUpdaters=skyview.executive.BatchCompatibility,skyview.ij.IJProcessor

Note the definition for the XMLRoot (the directory where survey XML
files may be found). When a value begins with a \$ the value of the
corresponding environment variable will be used but the line will be
ignored if the environment variable is not defined. This allows users to
override the default settings using environment variables using two
lines in the settings file, e.g.,

> Projection=Sin
>
> Projection=\$PROJ

will use a Sine projection unless the user overrides it by specifying
the PROJ environment variable.

## 5. Example requests.

1\.

java --jar skyview.jar position=3c273 survey=2mass-j,2mass-k,2mass-h

This returns three 300x300 pixel images named output1.fits,
output2.fits, and output3.fits with the survey default pixel size..

1a.

java --jar skyview.jar position=3c273 survey=2mass-j,2mass-k,2mass-h \\

quicklook=jpg nofits

Get the same images but only as JPEGs

1b.

java --jar skyview.jar position=3c273 survey=2mass-j,2mass-k,2mass-h \\

quicklook=jpg scaling=log

Get the same images but only as both FITS and JPEGs. Scale the JPEGs
logarithmically.

1c.

java --jar skyview.jar position=3c273 survey=2mass-j,2mass-k,2mass-h rgb

Get the FITS images along with a 3-color JPEG.

2\.

java --jar skyview.jar position=3c273 survey=2mass-j \\

scale=.0005 pixels=1200

This returns a single file 1200x1200 pixel file named output.fits with
pixels of 1.8".

3\.

java --jar skyview.jar position=3c273 survey=2mass-j \\

cache=/local/data/2masscache

This returns a 300x300 file but looks in the cache directory
/local/data/2masscache to see if needed survey files have been
downloaded there first. In the previous examples all survey files were
placed in the 'current' directory. Images are generated much faster if
needed survey data is already present in the cache. If the underlying
data is not already in the cache it will be placed in the specified
cache location.

4\.

java --jar skyview.jar position=3c273 survey=2mass-j \\

cache=/local/data/2masscache purgecache

This returns the same image as the previous request, but deletes any
survey files downloaded from the 2MASS site for this request. However
any files that might have been downloaded in previous requests are left
untouched.

5\.

java --jar skyview.jar position=3c273 survey=user \\

userfile=ff1.fits,ff2.fits,ff3.fits scale=.003 \\

sampler=Lanczos4 deedger=skyview.geometry.Deedger

This request looks at the three local files ff\[1-3\].fits and tries to
create a mosaic from them using a fourth order Lanczos resampler.
Boundaries between the input images are to be masked using the standard
deedger class.

6\.

java --jar skyview.jar position='horsehead nebula' \\

postprocessor=null output=horsehead \\

float coordinates=B1950

This asks for a DSS image of the Horsehead nebula but turns de-edging
off. The output image should use 4-byte reals and be in B1950
coordinates.

## 6. The Cache

When a user requests an image from a survey whose source files are on
another computer, the application first downloads the files onto the
local computer and then resamples the data. By default the downloaded
files are copied into the current directory and are left there when the
application is complete and serves as a cache for subsequent requests.
Often users make several requests near a given location, perhaps
changing the pixel size or resampling method used. When these subsequent
requests are made, the application notes that the needed files are
already downloaded and immediately begins resampling.

If a user is sure that a survey file is not going to be needed again, or
if space is at a premium, the user can request that the survey files be
deleted by specifying the PurgeCache setting. This will delete all files
downloaded for a given survey in the current request. However if
multiple files are needed for a given survey, then all files for the
survey will be downloaded and the output image produced before the
downloaded files are deleted.

While the advantages of keeping the survey files available can be
substantial, having them in the current directory can be a nuisance if
more than a few requests are made. In this case the user will likely
wish to specify a cache directory to save these files, so they do not
obscure other files in the current directory. A cache may be specified
in the settings file or in each command using the Cache setting to
specify one or more cache directories.

Users who create their own survey data sets (or who modify the XML
survey files distributed with the application) can create different
cache directories for each survey. By setting the cache directory in the
\<Settings\> area of the survey description the user specifies a default
cache directory which can be overridden on the command line. If the user
specifies a cache in the \<Images\> area, then this setting cannot be
overridden by the user. Note that more than one cache directory can be
specified. All of the cache directories are searched when looking to see
if a file is already available, however any files that are downloaded
will be placed in the first directory.

### 6.1 Caching the Digitized Sky Survey.

The Digitized Sky Survey data is handled somewhat differently than most
surveys. Rather than trying to download entire plates of data, which
would take forever even if it were permitted by the STScI servers,
*SkyView* requests small tiles from these images. It then builds the
image the user requests by mosaicking the tiles together. The tiles are
cached like any other survey. The headers for each tile indicate the
original image from which it was derived.

## 7. Dependencies on Remote Systems

While all data processing occurs in the local system, the
*SkyView*-in-a-Jar application may fail if remote resources are not
available. The underlying data for a few surveys are included inside the
JAR file (e.g., 408 MHz and EGRET). These are generally low resolution
surveys. The application will fail if it is unable to retrieve data for
other surveys. For many surveys that data is fetched from the *SkyView*
server at skyview.gsfc.nasa.gov. However the DSS, DSS2 and FIRST surveys
link to archives that the Space Telescope Science Institute, and the
2MASS and NEAT surveys use archives at JPL. A number of other surveys,
e.g., the SDSS, now use the VO Simple Image Access protocol, and link to
URLs described therein. The \<Images\> area of the survey description
will generally indicate the dependencies.

The only other remote dependency for the application is in the
resolution of target names. If the user specifies a target rather than a
pair of coordinates, the Name resolver/coordinate converter service at
the HEASARC is used to resolve this name into coordinates. The HEASARC
service in turn calls the SIMBAD and NED name resolvers. The HEASARC
service may also be used if the user enters the coordinates using
characters other than numerics, signs, colons, commas and decimal points
(e.g,

10h30m10.3s).

## 8. Compatibility with the SkyView Batch Interface

For the convenience of users of the old *SkyView* batch interface, the
*SkyView*-in-a-Jar application supports most of the arguments of that
interface insofar as they related to the generation of FITS files. The
following are supported as input settings:

  ---------------------------- ------------------------------------------
  ***SkyView* Batch keyword**  ***SkyView-*in-a-Jar setting**

  VCOORD                       Position

  SCOORD                       Coordinates

  MAPROJ                       Projection

  PIXELX,PIXELY                If both specified, converted to a Pixels

  EQUINX                       Equinox

  SFACTR                       Size

  COLTAB                       LUT

  ISCALE                       Scaling

  file                         Output
  ---------------------------- ------------------------------------------

The values are also converted appropriately. E.g., MAPROJ=Gnomonic is
translated to Projection=Tan.

Generally results from the new interface should be very similar to the
old *SkyView* interface. There is one major exception. The IDL code
which the old interface used ran almost entirely in single precision
arithmetic. The Java classes use double precision arithmetic exclusively
with an option for converting the final result to single precision.
Users must specify the Float setting to get single precision results.
The difference in precision and other small differences in the
algorithms mean that there can be small differences in the values
returned. E.g., when using a near-neighbor resampling, positions near
the edge of one pixel might move onto an adjacent pixel.

There format of the FITS headers differs in considerably between the two
versions. Substantially more information about the processing is
included in the new version including the files that were used in
generating the output mosaic.

## 9. SkyView-in-a-Jar Operations.

In this section we describe how the *SkyView* Java application works.
This includes short descriptions of some of the algorithms used.

The basic goal of *SkyView* is relatively simple. Given a set of one or
more existing images comprising a survey, *SkyView* generates a new
image in a user-specified geometry. The output user image may overlap
one or more of the survey images, and may overlap different images in
different locations. This section discusses how the application
accomplishes this task.

### 9.1 Getting defaults and user arguments.

When the application starts, a set of default parameters is established.
The java.executive.Settings class is used to convey the current
parameter settings. The default parameters are read in from a
configuration file or system resource. User arguments are then processed
and override any defaults. System parameters are stored in a HashMap but
both the put and get methods convert the key to lower case, so that the
keys are not case sensitive.

### 9.2 Updating Settings.

One or more classes may wish to look at the settings before processing
begins to fill in further defaults, to allow synonyms or for other
reasons. These classes should be specified in the SettingsUpdaters
setting. Currently the BatchCompability class allows syntax similar to
the old Batch interface while the IJProcessor fills in missing settings
when graphics have been requested.

### 9,3 Locating surveys.

Once the user arguments have been parsed, the application looks for
surveys. Using the default SurveyFinder there are four possible sources
of surveys:

-   The application searches for a survey manifest resource. This
    manifest gives the names of other resources or XML files where each
    file defines one survey. In this initial pass the XML is only parsed
    far enough to find the names of the surveys. Surveys can have
    several names. When the system tries to find the surveys the user is
    looking for the match will be done in a case-insensitive fashion.
    The source manifest is where the default surveys are normally found
    when the executable JAR file is used.

-   The second location where surveys may be found is determined by the
    setting for the SourceXML setting. This may be set on the command
    line, or if the user sets the environment variable SKYVIEW_SOURCEXML
    then the value of that variable is used. When the SourceXML is set,
    that directory is searched and each file of type .xml is treated as
    a survey definition file. Users can use this method to add a set of
    surveys to their *SkyView* implementation. It is also used when the
    *SkyView* application is run outside of the JAR file.

-   Users can specify one or more survey files directly using the
    SurveyXML setting. Each field in the SurveyXML is assumed to be a
    Survey definition file and is parsed.

-   Finally, the user can specify a 'User' survey by setting the
    SurveyFile setting. Each field of the SurveyFile is treated as a
    survey image file. Users can generate an image from this survey by
    using the survey name 'User'.

### 9.4 Looping over the surveys.

Once the set of available surveys has been determined, the application
loops over the surveys the user specified in the Survey setting. If the
name the user has specified is not found, then an error is signaled and
processing continues with the next survey.

When a survey is found, the corresponding survey definition file is
parsed. Part of the survey definition file is a set of survey default
settings, e.g., the default scale for the image, or whether the image
will be de-edged. These settings do not override settings already made,
so that survey settings do not override the overall defaults or user
defined settings.

### 9.5 Getting candidate survey images

The first step in processing a survey is determining a list of candidate
survey images that may be used in generating the output image. If a
survey uses the VO Simple Image Access Protocol (SIAP, see
http://us-vo.org), then the candidates are all images returned in the
initial SIAP request. If the survey explicitly lists the images, then
the application passes through these images and uses the ImageSize
characteristic to find images that might overlap part of the user's
image. If this is a request for the User survey, then all of the images
the user specified are candidates.

### 9.6 Building images.

At this point, a survey image is only a candidate for processing. Often
there will be many more candidates than will actually be used. If the
images are present locally this is not an issue, but it may seriously
delay processing if we download a number of images that are not actually
needed. To ensure that only needed data are retrieved from remote sites,
remote images are normally represented initially as proxy images. Proxy
images have the same geometry (or a very good approximation) as the real
image, but the image data is not filled in. If and when the application
decides to sample the data in the image, it downloads the remote data
and converts the proxy into a real image.

The SIA protocol allows for fields that define the geometry of the
images returned which makes it easy to build proxies without actually
retrieving data. For other surveys we find that the geometry of the
images is largely constant with only the center position changing. This
allows us to build 'spells' to enable the creation of proxy images and
their transformation to real images.

The Survey XML descriptor file controls this process. It can specify
either an explicit list of image files or spells that define the content
of the survey, or an ImageGenerator class that will create this list
dynamically. E.g., if the IRAS100 survey uses local data, then its
survey XML file lists 430 files explicitly. In the SkyView-in-a-Jar
distribution, the IRAS data is retrieved over the net, so the survey XML
file includes sufficient information to generate proxy images for the
survey. These proxies are used to find out which images are to be
resampled and which pixels in the output image are to be resampled from
which input image. Only when we actually begin resampling does the
program actually download the data.

The SDSS-I survey uses an ImageGenerator class that in turn uses the SIA
protocol to find candidate images around the user's requested location.
The SIA call returns sufficient information to generate proxy images so
we only actually retrieve the SDSS images we are going to use.

An ImageFactory class is also defined in the survey XML file. It shows
how to convert the file name/spell String into an actual image object.
The FitsImageFactory just reads in a FITS file, but the
CachingImageFactory first looks to see if files are present in the
cache, and if not creates a proxy image as described above.

Users can create their own ImageGenerator's and ImageFactory's to meet
special requirements for new surveys they might want to include.

### 9.7 Finding the best survey image for each output pixel.

Once the set of candidate images is determined, the application
determines the image to sample for each pixel in the output image. This
uses an object of the ImageFinder class. The default, BorderImageFinder
is described here. The position of the four corners of the output image
is determined for each of the candidate input images. The best candidate
image for each of the four pixels is then determined. The 'best' input
image is where the output pixel location is located in the image but
furthest from the edge of the input image.

E.g., consider first pixel (x,y=0,0) of the output image and assume
there are three candidate images each of which is a 500x500 image. The
position corresponding to the center of output pixel 0,0 is transformed
into the pixel coordinates of the three candidate images. If the pixel
coordinates corresponding to the output pixel in three candidate inputs
are (-80, 300), (40,40) and (250,35), then the second image is the best.
The output pixel location is not within the first image, and is only 35
pixels from the edge of the third, but 40 pixels from the edge of the
second.

If all four corners match the same input image, then that image is
assumed to be the best image for all of the interior pixels. If
different images are best (or perhaps there is no corresponding image
for one of the pixels), then the rectangle is broken up into four
sub-rectangles and the process is repeated recursively until we have
either checked each pixel individually, or we get common input images
for each corner of some sub-rectangle.

In the case where the output image is comparable to or larger than the
input images, the initial checking will be done on rectangles no larger
than half the size of the input images. When the input image selection
splits into sub-rectangles, any candidate image that was not found on
any of the four corners is not passed down to the next level of the
recursion.

Consider generating an all sky map from the IRAS100 survey which has 430
12x12 degree square images. The application first breaks the output
image into 6x6 degree squares and checks each of these rectangles
against all 430 images. In most cases it will not find the same best
image for all four corners of the 6x6 degree squares, so it next looks
at 3x3 degree squares. However, in this second step it only looks at
candidate images on which at least one of the four pixels at the
previous step was on the image (though not necessarily the best image).
So in this second stage we are typically looking at only three or four
candidates making the search much more efficient.

The end-point of this process is an integer array with the same
dimensions as the user output image but where the value at each pixel is
the best input image. Special flag values are used to indicate that this
output pixel is not matched by any survey image. An output pixel may
also be outside of the standard projection coverage, e.g., outside the
oval of an all-sky Aitoff projection, or the circle defined in the
Orthographic (SIN) projection.

In many cases the user may have selected images from a set of surveys
which have identical or near identical geometry (e.g., IRAS100 and
IRAS25, or 2MASS-J and 2MASS-K). These are called 'geometry twins' and
are identified in the survey descriptor files. If two geometry twins are
processed in succession, then the calculation of the best image from the
first twin processed is re-used for the later twin (or triplets, or
...).

### 9.8 Preprocessing

At this point the program allows for image pre-processing. The user can
define a class (or classes) that can modify the data that are used for
sampling. A preprocessor class has access to the input images, the index
associating images with output pixels and the output image. Only the
geometry of the output image has been specified, the data so far are
nil.

No preprocessing classes are currently provided. One useful class might
be a smoother that replaces the input images, with smoothed versions.

### 9.9 Validating the image.

Up to this point in the processing of the image, only the coordinate
system of the input image has been needed. To avoid downloading images
that may not actually be used, remote images use proxy images that do
not have data values associated. Even if the image is available locally,
only the FITS header is read rather than the data values if this can be
done efficiently. As we begin to process each survey image, the image is
validated, i.e., we download the image if it is a remote URL and then
populate the actual input data array.

While the proxy image should have a geometry very similar to the real
image, it may not be quite identical. If a request for a region is
repeated and the survey images were cached on the first request, then
the actual image geometry will be used at all stages in the second
request which may result is slightly different boundaries between the
regions sampled from the various input images.

### 9.10 Resampling setup.

Once the 'best' image for each output pixel has been selected, the
program begins to process each input image. For some samplers there is
some processing of the input image done before any resampling occurs.
E.g., the spline resampler needs to calculate the spline coefficients to
be used. In this case if the input image is much larger than the output
image, then spline coefficients may only be computed on a sub-region of
the input. The minimum and maximum x and y values for the output image
that are being sampled in this input image are computed. These bounds
are projected into the input coordinate system and the spline is
computed only for this sub-region. Currently this behavior is enabled
only for tiled surveys.

### 9.11 Sampling in energy.

If the input survey has depth in the energy dimension, the data is first
sampled in energy according to the Ebin's specification before spatial
sampling. A default specification is normally included in the survey
default to produce a 2-d output image. Thus unless the user specifies
that they want a 3-d output image, they get a 2-d image.

If there is no energy dimension to the data, this step is skipped.

### 9.12 Sampling in space.

The program then loops over the output pixels associated with the
current input image and computes the value using the selected resampler.
For most resamplers the center of the output pixel is projected into the
plane of the input image. For the clipping sampler, the corners of the
pixel are projected. The output pixel is then populated with the
resampled value according to the requested algorithm. If the output
image has depth in the energy dimension, the sampling is performed at
each output energy channel.

Currently the spline sampler cannot process 3-d images.

### 9.13 Post-Processing

After the data have been resampled, post-processing may be performed.
The interface for post-processing is exactly the same as for
pre-processing, however at this point the output image has been
populated and we would anticipate that most post-processing will perform
some filtering of the output image while preprocessing is expected to
primarily affect the input image or images. Examples of post-processor
are de-edging and graphics processing

#### 9.13.1 De-edging

Since survey data may have different background values in the different
survey images, the edges of the image may show up as an unsightly
artifact. If the user wishes to minimize the edges, then a de-edger may
be run on the output image. .

The algorithm used by the default deedger attempts to minimize
discontinuities along borders. The output image is divided into regions
defined by the input image from which the pixels were sampled. These
regions are placed into adjusted and unadjusted sets. The region with
maximum number of pixels is placed in the adjusted set and all other
images are initially unadjusted. The program then looks for the longest
border between an adjusted and unadjusted region. Borders are defined by
looking at each pixel and seeing if any of the four neighboring pixels
is from another region (diagonals are not considered). The median of the
shifts as we move across the border from the adjusted to the unadjusted
regions is computed. An offset is applied to the unadjusted region to
set the median shift across the border to 0. The unadjusted region is
moved into the adjusted set, and the process iterates until all regions
have been adjusted. Other classes use somewhat different algorithms to
compute the offsets for images: use the average rather than the median
shift at the border, adjusting the medians of all pixels that come from
an image, not just the boundary pixels.

The FITS headers include information on the adjustments made when
de-edging is applied.

#### 9.13.2 Graphics Processing

All graphics outputs are also produced in post-processing. Appropriate
functions in the ImageJ library are called to produce the desired data.
Graphics procdssing does not affect the FITS data. If Min or Max
settings were given, then any values below or above the limits are
replaced by the limit value. The data is then scaled using the
appropriate scaling method. Logarithmic (Log) and Square-root (Sqrt)
scaling scale negative values to 0 (or the minimum positive value for
log). The result are images with values ranging from 0 to 255. These
data are then converted to the requested graphics output.

If users request an RGB image from three input surveys, then each of
these surveys is processed in turn and the scaled results are stored
until the last survey is processed. Then the three images are combined
to create a single RGB JPEG file.

### 9.14 Data conversion and writing the FITS file.

All of the internal computations are done with the data as a
one-dimensional double array of values. Just before writing the data
out, the application checks to see if the user wished to have only
4-byte reals (float's in C or Java-speak) rather than the default 8-byte
data (double's). If so the data is converted. The program then 'curls'
the data into the appropriate dimensionality and uses the nom.tam.fits
library to write the FITS image. The survey descriptor defines
survey-dependent information that is included in the FITS header.

The user can elect not to create a FITS image by specifying the NoFITS
setting.

### 9.15 Cache cleanup. 

If a user requested data that was not present in local files, this data
is first downloaded into the first cache directory (the current
directory by default). By default downloaded survey files are left for
possible use in subsequent requests, but if PurgeCache has been set,
then these files are deleted as the processing for each survey is
completed. However only the files actually downloaded during this
request will be purged. Files already present in the cache will be left
untouched.

## 10. Survey Definition File

Each survey (other than the 'User' survey) used in SkyView is defined by
a survey definition file. This is an XML file that pulls together all
information needed to use the survey. This section describes the
structure of the file. \[Note: A user can define SurveyFinder object
with behavior that they specify.\]

There is no formal schema for the survey file format but we suggest the
following order for the top elements of the file.

### Survey

ShortName

Name

Description

Settings

MetaTable

OnlineText

FITS

Images

### 10.1 ShortName

The short name element gives one or more short names for the survey.
Short names are used as the values of the Survey keyword in the
SkyView-in-a-Jar application and therefore it is recommended that they
not contain embedded blanks. If multiple short names are to be specified
they are separated by commas. All survey description files are read at
program startup until the short name is found, so putting this first can
speed up the program a little.

Examples:

\<ShortName\>DSS2R\</ShortName\>

\<ShortName\>EGREThard,EGRET100-10000\</ShortName\>

### 10.2 Name

The name element gives a longer name for the survey generally spelling
out acronyms and such that may have been used in the short name.

Example:

\<Name\>Two Micron All-Sky Survey: K band \</Name\>

### 10,3 Description

This gives a text description of the survey. This may include HTML and
if so should be coded as a CDATA element.

Example

\<Description\>

\<\![CDATA\[

This LISA Galactic survey is a low-resolution image

of the gravitational background in

the Galactic plane as described in \<a href=someurl\>Lisa

Galactic Plane Handbook

\</a\>

\]\]\>

\</Description\>

### 10.4 Settings

The settings element is used to specify survey specific settings. Within
the settings element there may be 0 or more sub-elements of the form

\<key\>value\</key\>

When processing of a specific survey begins, the Settings element is
parsed and the Settings hash is updated with any key/value pairs found.
The case of the key is not distinguished but case may be important in
the value. Note that XML parsers require that the opening and closing
case of the keys be consistent within the file.

Common survey specific settings include the default image scale (Scale),
other surveys that have the same geometry (GeometryTwin), the default
energy binning for 3-d surveys (EBins), and post-processing options,
notably the de-edger.

Survey settings will not override existing user specified settings.

\<Settings\>

\<Scale\> 0.003 \</Scale\>

\<GeometryTwin\>SurveyA,SurveyB,SurveyC\</GeometryTwin\>

\<Deedger\> skyview.geometry.Deedger \</Deedger\>

\</Settings\>

Since the survey settings do not override user specified settings, the
default de-edging of this survey will be turned off when the user
specifies Deedger=null.

### 10.5 MetaTable

The metatable element includes a set of metadata elements that give an
overall description of the survey. *SkyView* attempts to give some
common information about all surveys, energy range, resolution, ... and
these are grouped in the metatable.

The metatable information is normally included in any FITS file produced
and elements may be displayed in other interfaces.

Example:

\<MetaTable\>

\<Provenance\>

NASA IPAC/Jet Propulsion Laboratory

\</Provenance\>

\<Copyright\> Public Domain \</Copyright\>

\<Regime\> Infrared \</Regime\>

\<NSurvey\> 4 \</NSurvey\>

\<Frequency\> 3-30 THz \</Frequency\>

\<Coverage\> All-sky \</Coverage\>

\<Scale\> 0.025 deg/pix \</Scale\>

\<Units\> MJy/sr \</Units\>

\<Resolution\> 2' \</Resolution\>

\<Coordinates\> Equatorial \</Coordinates\>

\<Projection\> Gnomonic(TAN) \</Projection\>

\<Equinox\> 1950 \</Equinox\>

\<Epoch\> 1983 \</Epoch\>

\<Reference\>

\<\![CDATA\[

Wheelock, et al., 1991, IRAS Sky Survey Atlas Explanatory

Supplement.

\]\]\>

\</Reference\>

\</MetaTable\>

### 10.6 OnlineText

The online text element is used to include text that is to be shown on
Web pages associated with a generated image. The online text may include
HTML tags and if so should be enclosed a CDATA element. Variables
prefixed by \$ will be substituted for in the text by the appropriate
values. These include:

\$ra The right ascension of the center of the image in decimal degrees

\$raH The hours of right ascension

\$raM The minutes of right ascension

\$raS The seconds of right ascension (including fraction)

\$dec The declination of the center of the image in decimal degrees

\$decD The degrees (and sign) of declination

\$decM The minutes of declination

\$decS The seconds of declination (including fraction)

\$sizeD The requested size of the image in degrees.

\$sizeM The requested size of the image in minutes.

\$sizeS The requested size of the image in seconds.

Example:

\<OnlineText\>

\<\![CDATA\[

\<a
href=http://somewhere/cgi-bin/query?POS=\$ra,\$dec&SIZE=\$sizeD\>Link
\</a\> to the associated source catalog.

\]\]\>

\</OnlineText\>

No software currently uses this element and no data is supplied in these
elements in the survey descriptions included in the Jar.

### 10.7 FITS

The FITS element includes information to be included in the FITS header
generated with the image.

Example:

\<FITS\>

\<\![CDATA\[

SURVEY = 'IRAS 100 micron'

BUNIT = 'MJY/SR ' / INTENSITY

COMMENT Note that the values are not adjusted for any change in pixel

COMMENT size from the original pixel size of 90 x 90 arcseconds

BLANK = -2000000000 / TAPE VALUE FOR EMPTY PIXEL

ORIGIN = 'JPL-IPAC' / INSTITUTION

TELESCOP= 'IRAS ' /

INSTRUME= 'ISSA-FLD' / IRAS SKY SURVEY ATLAS

EDITED = T / SCANS EDITED

APPCAL = T / CALIBRATION CORRECTION 25 MICRON

DE-ZODY = T / DE-ZODIED IMAGE

GLBL-D = T / APPLIED GLOBAL PARAMETERS

LOCAL-D = T / LOCAL DESTRIPER

ASBLANK = T / ASTEROID BLANKING

\]\]\>

\</FITS\>

## 11. The \< Images\> Element 

The main business of the survey file is in the Images element and so we
give it a whole section to itself. There are two alternate
configurations: an explicit list of the images in the survey, or a link
to a class that will generate a list of images for a given user request.
Most of the fields in the Images element (with the exception of Image
elements) are parsed when survey processing begins and used to update or
set entries in the Settings hash. However, unlike the fields in the
Settings element, these settings override any existing settings.

### 11.1 Explicit Image Lists

In this case, the Images element will contain a set of Image elements.
Each element has a text value with four blank delimited tokens: the
filename or spell, a longitude and latitude, and the epoch of the image.
The coordinate system for the longitude and latitude can be specified in
the "SurveyCoordinateSystem" setting and defaults to J2000. In addition
to the Image elements there should at a minimum be an ImageFactory
element and an ImageSize element. The image size gives the size in
degrees of the smaller dimension (if not square) of the images. This is
used in the process of determining the best image for each output pixel.

The ImageFactory gives the class which given the appropriate spell or
file name creates the image. The skyview.survey.FitsImageFactory takes a
filename and simply reads the file to create the input image. If a
\<FileNamePrefix\> element is included Images element, then this prefix
is prepended to the file name in the Image element before being passed
to the FitsImageFactory.

The skyview.survey.CachingImageFactory assumes that it is being given a
spell that tells it both how to retrieve the data as a URL as well as
sufficient metadata to create a proxy image. The spell consists of 10 or
12 comma delimited fields. These are:

1.  The URL to retrieve the data from

```{=html}
<!-- -->
```
1.  The file name to store the cached file as

2.  The longitude of the center of the image

3.  The latitude of the center of the image

4.  The projection used in the image

5.  The coordinate system used in the image

6.  The width of the image in pixels

7.  The height of the image in pixels

8.  The width of a pixel in degrees

9.  The height of a pixel in degrees

..or..

9-12. The CD matrix elements for the image.

For projections (Aitoff, Cartesian and CSC) where the reference value is
normally fixed, the third and fourth tokens are the pixel offsets for
the image, while for other projections the reference pixel is assumed to
be at the center of the image.

The user familiar with FITS will note the similarity of fields 3-10 (or
12) to standard FITS WCS keywords. Note that the spell does not need to
use the same coordinate system as the other fields in the Image
elements.

If the SpellPrefix or SpellSuffix values are specified in the Images
element, then the Image spell string is appropriately extended. Usually
much of a spell is constant for a given survey.

### 11.2 Image Generators

Rather than specifying each individual image, the survey file can
describe an ImageGenerator class that will generate the images. An Image
generator can generate either files or spells.

There are specialized image generators for the DSS and 2MASS surveys.
Users may wish to examine these classes for extension to other special
surveys, but the most useful generator is likely to be the
SIAPGenerator. The SIAP generator uses the Virtual Observatory Simple
Image Access protocol and can be adapted to use many of the existing
SIAP services with appropriate entries in the Images element.

The key fields are:

-   SiapURL: defines the base URL for the Simple Image Access service.

-   SiapProjection: The projection used in images returned by the
    service

-   SiapCoordinates: The coordinate system used in images returned by
    the service

-   SiapNaxis: The size (in pixels) of image returned by the service

-   SiapScaling: The size (in degrees) of the pixels returned by the
    service

-   SiapMaxImages: The number of images returned to include as
    candidates.

Alert readers will note the correspondence of most of the fields to the
spell parameters and to the FITS WCS fields. SIAP services can return
WCS information for each image explicitly and to the extent that they do
so (e.g., almost all return the size of the image in pixels), the user
need not supply this information. However many (most) SIAP services do
not supply all needed information. The fields above remedy any deficit.

Not all SIAP services are good candidates for immediate inclusion as a
service. *SkyView* will use all images returned as candidates even if
the images are quite heterogeneous. Only SIAP services that return
relatively homogeneous images can be used with some kind of initial
filtering. However it is often easy to modify the SIAPGenerator to do
such filtering and we anticipate that this class will have filtering
capabilities added.

The third example below shows the power of the SIAPGenerator. The entire
SDSS survey is included as a survey with just a few lines of text.

### 11.3 Example \<Images\> elements

*Listing local files:*

\<Images\>

\<FilePrefix\>

/surveydata/iras/iras100/

\</FilePrefix\>

\<ImageFactory\>

skyview.survey.FitsImageFactory

\</ImageFactory\>

\<ImageSize\> 12.5 \</ImageSize\>

\<Image\> i001b4h0.fits 0. -90. 1980.00 \</Image\>

\<Image\> i002b4h0.fits 0. -80. 1980.00 \</Image\>

\<Image\> i003b4h0.fits 45. -80. 1980.00 \</Image\>

\<Image\> i004b4h0.fits 90. -80. 1980.00 \</Image\>

\<Image\> i005b4h0.fits 135. -80. 1980.00 \</Image\>

... 425 more Image elements ...

\</Images\>

*Listing remote URLs:*

\<Images\>

\<SpellPrefix\> http://skyview.gsfc.nasa.gov/survey/iras100/images/

\</SpellPrefix\>

\<SpellSuffix\> ,Tan,B1950,500,500,0.025,0.025 \</SpellSuffix\>

\<ImageFactory\> skyview.survey.CachingImageFactory \</ImageFactory\>

\<ImageSize\> 12.5 \</ImageSize\>

\<Image\> i001b4h0.fits,i001b4h0.fits,0.,-90. 0. -90. 1980. \</Image\>

\<Image\> i002b4h0.fits,i002b4h0.fits,0.,-80. 0. -80. 1980. \</Image\>

\<Image\> i003b4h0.fits,i003b4h0.fits,45.,-80. 45. -80. 1980. \</Image\>

\<Image\> i004b4h0.fits,i004b4h0.fits,90.,-80. 90. -80. 1980. \</Image\>

\<Image\> i005b4h0.fits,i005b4h0.fits,135.,-80. 135. -80. 1980.
\</Image\>

... 425 more images ...

\</Images\>

*Using an Image generator.*

\<Images\>

\<SiapURL\>

\<\![CDATA\[

http://casjobs.sdss.org/vo/DR3SIAP/siap.asmx/getSiapInfo?FORMAT=image/fits&BANDPASS=I&

\]\]\>

\</SiapURL\>

\<SiapProjection\> Tan \</SiapProjection\>

\<SiapCoordinates\> J2000 \</SiapCoordinates\>

\<ImageFactory\> skyview.survey.CachingImageFactory \</ImageFactory\>

\<ImageSize\> 0.25 \</ImageSize\>

\<ImageGenerator\> skyview.survey.SIAPGenerator\</ImageGenerator\>

\</Images\>

## 12. A Simple Survey Definition File

While a survey XML definition file can be complex, most data is
optional. A minimal survey definition need only include the short name
of the survey, a default scaling, the image size and the names and
locations of the included files.

\<Survey\>

\<ShortName\> MySimpleSurvey \</ShortName\>

\<Settings\>

\<Scale\> .1 \</Scale\>

\</Settings\>

\<Images\>

\<ImageSize\> 10 \</ImageSize\>

\<ImageFactory\> skyview.survey.FitsImageFactory\</ImageFactory\>

\<Image\> file1.fits 0. 0. 2000 \</Image\>

\<Image\> file2.fits 10. 0. 2000 \</Image\>

\<Image\> file3.fits 20. 0. 2000 \</Image\>

\</Image\>

\</Survey\>

This describes a survey with three images along the equator (at RAs of
0, 10 and 20 degrees) which have a minimum dimension of 10 degrees and
0.1 x 0.1 degree pixels.

## 13. Contents of the JAR file

The SkyView JAR file contains files from a number of directories as well
as indidual files used by the program. This section discusses the
content of the JAR for users who may wish to create their own customized
versions of the JAR. You can view the contents of the JAR file using the
command jar --tf skyview.jar.

### 13.1 The Class Files

Class files are found in three directory trees:

-   skyview/... contains the class files for the class files developed
    in *SkyView*. This includes all the code relating to geometric
    transformations, image surveys and the main program for the JAR
    file.

-   nom/... contains the methods for reading and writing FITS files and
    utility I/O functions.

-   ij/... contains the classes and a few data files) for ImageJ.

### 13.2 Survey Data and Metadata

The JAR file contains metadata descriptions for many surveys and actual
survey data for a few. Metadata descriptions in the format described
above are found in surveys/xml. FITS data for a number of surveys is
found in surveys/data.

The survey manifest file gives a list of all of the surveys included in
the JAR and is found in surveys/survey.manifest.

### 13.3 Control Files

A number of control and miscellaneous files are found in the JAR.

-   The skyview.settings files contains the default settings for the
    program.

-   IJProps.txt contains settings used by ImageJ.

-   The MANIFEST/MANIFEST.MF file is included in the JAR using a command
    like jar fm skyview.jar manifest.fil (the JAR command renames the
    file when it is inserted). It contains a single keyword value pair
    that gives the class which is to be used when the JAR is executed
    (currently skyview.executive.Imager).

-   The onlineinfo.txt file contains help text which is displayed when
    the program is invoked without any arguments.

### 13.4 Source code

Source code is found in the source/... hierarchy for all Java classes
defined in the JAR file.