# Getting a quick spectrum with default parameter settings¶

There are three ways to run the program. The preferred method for me (the developer) is while using an ipython shell and the how-to was briefly shown earlier as Running from the command line. The second method is as a command-line call, while the third method would be to run within a Python shell. The command line call has not been updated since version 1.0, but is calling the revised spectral extraction code.

## Preparations¶

Before starting the spectral extraction, the data for your observation(s) needs to be available on your system. Besides the image files, the spacecraft attitude file and its directory should be available. Although some options were built-in to the program for other arrangements, the only known way that works has the same directory and file structure as that distributed by the Swift archive:

<obsid>/
<obsid>/auxil/sw<obsid>pat.fits  # these files may be compressed
<obsid>/auxil/sw<obsid>uat.fits
<obsid>/auxil/sw<obsid>sat.fits
<obsid>/uvot/image/sw<obsid>ugu_rw.img (optional)
<obsid>/uvot/image/sw<obsid>ugu_dt.img (required)
<obsid>/uvot/image/sw<obsid>ugu_sk.img
(example for UV GRISM, *ugv_sk.img for V GRISM)
<obsid>/uvot/image/sw<obsid>uw1_sk.img (if present)
<obsid>/uvot/image/sw<obsid>uw2_sk.img (if present)


The <obsid> is typically of the form "00032323001", and is one of the required inputs needed. During the ground processing at NASA-GSFC, the initial attitude file sw<obsid>sat.fits may be updated to sw<obsid>uat.fits, or sw<obsid>pat.fits based on further analysis.

note:

Start the program from the <obsid>/uvot/image/ directory to get all files written to one place. The program supports a directory option, but writes also to the local directory.

Alternatively, you can leave the original Swift files where they are and do all processing in a dedicated directory folder which will only contain the products of the processing.

The second most important item needed is the source position in RA, Dec (J2000) decimal degrees (not in sexagesimal).

Finally, the FITS extension of the spectrum image (<obsid>/uvot/image/ file) is needed; when not given it defaults to 1.

The analysis uses the detector image *_dt.img files which have been distortion corrected. This means that the same correction was applied to the grism image as was found for the lenticular filter images, but additional distortions remain in the grism spectra.

IMPORTANT: Internet access is needed so that the USNO-B1 on-line catalog can be queried for a list of stellar data in the field.

A quick inspection of the sky images *_sk.img is useful to make sure the spectrum exposure was correct. There are several other pitfalls, like overlapping orders which can be diagnosed by using DS9 in combination with a DSS image. That is discussed elsewhere in Basics of UVOT Grism analysis.

## Extracting with IPython¶

The ipython shell is more versatile and user-friendly in interactive sessions, with command line finish and recall, for example. A session can be started from the <obsid>/uvot/image/ directory, or use cd <obsid>/uvot/image/  from within the ipython shell to go to the directory. Use the –pylab argument to load matplotlib for the session, and define the required parameters:

ipython --pylab
from uvotpy import uvotgetspec
ra, dec = 123.45678, +65.789012
obsid = "00032109002"
ext = 2


We will use the getSpec program from the uvotpy.uvotgetspec module of the uvotpy package. We can now do a simple call to the program. Assuming the obsid and position are all correct:

uvotgetspec.getSpec(ra,dec,obsid,ext, fit_second=False, clobber=False)


I have set here one more parameter “fit_second” to “False”, since this can cause problems when the second order completely overlaps the first order, i.e., is not offset in the cross-dispersion direction. An offset will have an anchor position for the first order listed in the output not close to (1100,1100).

Three graphs will appear.

• The first one to quickly view the extraction is positioned approximately right, and crosses are plotted at about 200A offsets at the estimated location of the spectrum.
• In the second graph the extracted raw data in the form as total counts, i.e., (no background subtraction, and not as rates), aligned with the image section obtained after rotating to the dispersion). Also, a very rough guess of the second order counts is made based on those in the first order. It tends to over-estimate, sometimes as much as a factor of two.
• In the third graph, the flux calibrated spectrum.

It should be noted that the flagging of bad areas is at the moment pretty bad, and needs to be looked at again. I noticed that when running uvotgrism from the command line the figures don’t always show.

The spectra will be written to a file which includes a data extension for use with XSPEC. However, the RMF file for XSPEC is not produced automatically, since it involves a very slow piece of code. For that set the getSpec parameter write_RMF = True. The RMF is useful, since the spectral resolution gets worse to the red, and is especially affecting wavelengths above 400nm in the UV Grism spectra.