How to run the gov.fnal.eag.sim demonstration code

Make sure that the java executable is in your path. Use its -version flag to find the version. You need to have version 1.5 or higher for the code to work.
```
$ java -version
java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Client VM (build 1.6.0-b105, mixed mode, sharing)
```
Put all of the .jar files in a directory. Here, we assume that you have assigned the variable LIB_DIR to point to that directory.
Put the pauRunner.sh file in a directory that is in your path.

Run the command pauRunner.sh, and see that it tells you this:

$ pauRunner.sh
Usage: pauRunner.sh LIB_DIR className [arguments]
If you want more memory, use -Xmx1000m between LIB_DIR and className to get 1 Gbyte of memory

Run the class gov.fnal.eag.sim.pixel.MakePixeledImage with the default settings:
```
$ pauRunner.sh $LIB_DIR gov.fnal.eag.sim.pixel.MakePixeledImage
```
That made fhe file defaultMakePixeledImage.fit which you can display with ds9.
Run the same program with one additional parameter, which gives the name of the properties file that controls the program. Here are three sample parameter files:

The command to run the ellipses version is this:

$ pauRunner.sh $LIB_DIR gov.fnal.eag.sim.pixel.MakePixeledImage ellipsesMakePixeledImage.par

Here is a description of each parameter in the .par files. If you omit a parameter, the default value will be used. ObjectGrid for a grid of objects; Zucca for galaxies

parameter name	default value	description
a7	0.0	non-linear term for sky to pixel projection
arcsecPerPixel	0.1	pixel size in arcseconds
baseFileName	defaultMakePixeledImage	output file will be have .fit appended to this name
catalogSeedIndex	3	controls the random number tree that defines the truth catalog
colRef	250	reference column position in the detector
countsPerSecondAt20th	1000	the number of counts/second for the telescope+filter+dector for a 20th magnitude object
decBore	30.0	declination of the center of the focal plane
detectorRotationDegrees	0.0	rotation of the detector around its reference posision
detectorXPositionMeters	0.0	location of the detector reference row,col position in the X direction (meters)
detectorYPositionMeters	0.0	location of the detector reference row,col position in the X direction (meters)
doPoisson	true	whether to add poisson noise to the image
expTime	100	exposure time in seconds
filterName	pegase-r	the name of the filter
gridAbsMags	19	absolute magnitude of all grid objects
gridCenterDecs	30.0	declination (degrees) of the grid of objects
gridCenterRas	20.0	right ascension (degrees) of the grid of objects
gridDeltaArcsecs	30	separation in arcseconds between grid objects
gridDistancesAreRedshifts	false	distances are in redshifts (if true) or pc (if false)
gridLfBandpass	pegase-r	filter that defines the luminosity of grid objects
gridObjectReferenceRedshifts	10	distance to grid objects
gridObjectShapes	profile gauss 0.0 0.0 15	defines the shape of grid objects: profile ellipticity theta nShapeletOrders
gridObjectSizeArcsecs	0.5	scale length of grid objects in arcseconds
gridSEDNames	CWW_E_ext	spectrum of grid objects
gridSizes	3	diameter of grid, in number of objects
ImageRepositoryDirectory	.	where to write the answer
luminosityFunctionNames	ObjectGrid
maxRedshifts	10.0	redshift maximum for objects (use 1.0 for Zucca)
metersPerPixel	25e-6	pixel size in meters
minRedshifts	10.0	redshift minimum for objects (use 0.01 for Zucca)
nCol	500	number of columns in the detector
noiseSeedIndex	4	defines the tree of random numbers for poisson and read noise
nRow	500	number of rows in the detector
pixelSizeArcseconds	0.25	size of the pixels in arcseconds
psfFileName	null	file name for PSF convolution kernel
raBore	20.0	right ascension of the center of the focal plane (degrees)
readNoiseElectrons	0.0	read noise in electrons
rowRef	250	reference row in the detector
skyMagPerArcsec2	25.0	sky brightness