DUDE

DUDE is a program written by David Kirkman. The program is written in java, and will take fits files and ascii files will fit continua, fit lines, all kinds of neat data things.

Here are some notes that I have compiled on using the program.

If you get a bunch of java errors:

sudo update-java-alternatives -s java-6-sun

Cheat sheet of the most useful shortcuts:

Resizing To set the minimum WAVELENGTH k
Resizing To set the maximum WAVELENGTH l (lowercase L)
Resizing To set the minimum FLUX b
Resizing To set the maximum FLUX t
Resizing Set min FLUX to 0 0 (zero)
Continuum Add continuum points c
Continuum Delete continuum points v
Continuum Move continuum points m

How to use the Program

To run on Moebius:

java -jar Desktop/Sundrop/dudefull-2008-08-27.jar &

with a special atom.dat

java -Ddude.atom=/home/jonathan/Desktop/DATA/addtoatom.dat -jar /home/jonathan/Desktop/Sundrop/dudefull-2008-08-27.jar &

This will load the program.

Click:

File
-    New

Type random characters, the title will not be saved.

File
-    Add Spectrum (or Add Ascii Spectrum depending)

If fits files, pick appropriate Flux and Err files (we have error files so uncheck that box).

Resizing the Window

View
-    New Standard View

Now this is the fun part. Kirkman tweaked it so that this really runs nice. You have to resize the window. So the following commands do a beautiful job of getting this done quickly.

First, keep in mind that the program is taking where your mouse is as the point at which to do the following commands. So pay attention to the cursor as your type away at the keyboard.

Resizing To set the minimum WAVELENGTH k
Resizing To set the maximum WAVELENGTH l (lowercase L)
Resizing To set the minimum FLUX b
Resizing To set the maximum FLUX t
Resizing Set min FLUX to 0 0 (zero)

Continuum Points

Next, we add Continuum Points.

Position the mouse where you want the continuum points, and press —> c

You should start with 3 continuum points to the left, and 3 to the right, of the area that you want to optimize. Sprinkle through the rest of the section a few continuum points (along the general curve of the background).

Continuum Add continuum points c
Continuum Delete continuum points v
Continuum Move continuum points m

Important Point
After you have the continuum points in roughly the correct areas make sure to lock the x-values of the continuum points. Again, Kirkman comes through with a slick way of doing this.

Click:

Model
-    Continuum
    -    Toggle Lock x for all points

Add Absorbers

Click on the Absorber tab (one of the 3 tabs just under the menu options; File, Edit, View, Model, Optimize)

1. Find the absorber from the list (our case either Fe II 1608, or "??").

2. Click "A"

3. Click where you guess the center of the component is for your absorption line.

4. Move column density and velocity dispersion until it looks close.

Optimize

Remember that the x-values of the continuum points must be locked!

Optimize
-    Add Region

click left and right of the absorption lines (The spectrum will turn pink between the points that you clicked).

The program will optimize the continuum points in the pink region as well.

Optimize
-    Optimize
    -    Levenberg-Marquardt

Important note: Kirkman's made it so that the Chi squared is printed out in the terminal that launched the Dude program.

Exporting Useful Things

Another important thing to remember!
The default name for whatever you're about to export is the same as the last file you loaded! Be sure to type something new in or you'll overwrite files!

Export Ascii Absorbers
(This will export the relevant info on the absorbers that were fit.)

Export Ascii Continuum Points
(This exports the relevant continuum points that were added — if you want to recreate the fit you made using Dude, you need the continuum points that you used).

Export Ascii Spectrum
(This exports the wavelength, flux, error, fit, and continuum that Dude fit.

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