XDSPEC

Name

xdspec

Purpose

End-to-end reduction tool for OSIRIS XD spectral data.

Description

This program handles all steps of processing raw OSIRIS XD spectral data
to create final averaged output spectra. This will work quite well for
data on single point sources. If the objects are extended or if there
are more than one object, you need to do the reductions by hand.

Calling Sequence

xdspec

Inputs

Optional Input Parameters

Keyword Input Parameters

Unless otherwise indicated, these options are all flags.
ABSPOSCAL - Run through the absolute position calibration step.
ADDPATH - String of directory name to prepend to the DIRLIST for a
location to look for the raw data. The same restriction
applies to this as to DIRLIST.
ALLCAL - Run through all the calibration steps.
ALLSPEC - (Re)compute all spectral extractions.
AVGSPEC - Force (re)computation of final average spectra.
DIRLIST - String array list of directories for where to search for
raw data. Do NOT include the final directory that is
the same as the current directory and the root of the
raw data files.
FINAL - Enable final spectral extraction, this step combines any
bad pixel masks and creates final mask (if not already
present) and then extracts all spectra.
FLUSH_INFO - Flush all remembered information.
GAUSSCOR- Correction factor from the directly computed image FWHM (per order)
See OPTSPEC for a more detailed explanation.
GROUPCHECK - Flag, generate a summary plot of all spectra against their
group leader.
MASKTHRESH - When using a final mask image, you can adjust the mask
threshold with this keyword. The mask image records the
fraction of the time that a given pixel is recorded as
being "bad". This fraction varies between 0.0 and 1.0.
The default is to mark pixels bad that are seen to be bad
more than 4% of the time. In other words, MASKTHRESH=0.04
is the default.
NOSPEC - Inhibit any spectral extraction processing.
PLOTRANGE - Two element vector, [start,stop], frame numbers to generate
postscript plots for.
PLOTS - How many and how much to plot. (only for optspec plots)
0 - All plots generated.
1 - No plots at all.
2 - Show strip image, average profile, order profiles (default)
QUEUE - (String) Print queue to send postscript plots to. If this
is not provided, then the idl.ps file is not spooled to
a printer and is left behind when xdspec finishes. If you
give a queue name, the idl.ps file is deleted after the
file is spooled for printing.
RELPOSCAL - Run through the relative position calibration step.
SLOPECAL - Run through centerline slope calibration step.
WAVECAL - Run the wavelength calibration steps on each order.

Outputs

All output is either to the various plot screens or to files.

Keyword Output Parameters

Common Blocks

COM_XDSPEC - Used to store information from one invocation of xdspec to
the next.

Side Effects

Restrictions

If you use an 's' flag to eliminate an image and its spectrum from the
output products, you will not necessarily get this image as a mate in
cases where you might like it. You will almost always need to tweak
the mate in the .tbl file by hand in these cases.

Procedure

This program assumes (and requires) that the current directory is NOT where
the raw frames are to be found. The raw frames are in some other location
and have no other files with them. This allows you to have the raw data
in a location where you do not have write permission (ie., CDROM). All
of the resulting files from running xdspec are written to the current
directory and directories beneath there.
Also, for simplicity of bookkeeping, I have assumed that the root of the
raw data file names is the same as the directory where you are running
xdspec and where the data live. For example:
Data files of the form: 980115.001
Current directory: /usr/results/980115/
Data directory: /usr/data/980115/
In this case '/usr/data' should be in the DIRLIST or added with ADDPATH
(if it isn't already present).
If there are no flat field calibration frames on this night, you must use
calibration specifications and flat fields from another night in that
run. In this case, as you start XDSPEC you get a flat field selection
popup window. Use this tool to browse through other nights until you
find an appropriate calibration file. In selecting the flat you are
actually selecting that flat and its associated files.cal specification
file. In this case you probably shouldn't fiddle with _anything_ in
the files.cal and if the original ever changes, you should probably start
all over from scratch on any other nights that use the same stuff.
You _can_ re-run the wavelength calibration steps in this case but it's
probably not a good idea. Once you select the flat field, processing
continues and there's very little that needs to be done on the calibration
steps (actually nothing at all).
During the wavelength calibration steps, here are the mouse operation
options: (1st:sky spectrum) (2nd:synthetic)
left measure nearest line grab nearest strong line
middle delete nearest point nothing
right done abort this line
Here's the typical "flow" of running this program:
xdspec <-- Initial call, sets up calibration information, and
extracts initial spectra. Run this as many times
as needed to get a complete set of initial spectra.
xdspec,plotrange=[1,NNN],queue='printer name'
this will generate the summary plots for all the
spectra. Do only when all are done. You then review
the plots with an eye toward spectra that should be
removed from the averages. You mark one to be skipped
by replacing the second column flag character
by an 'x' (to exclude). After all have
been marked, proceed to the next step ...
xdspec,/final <-- Final processing, combines bad pixel maps, reextracts
the spectra and generates final averages. You are done
with this program at this point.
Note, you can ignore any spectrum in the tbl file by marking it with an
'x' in the second column in the table. It will do no good to delete the
line from the table as the line will come back. 'x' marks it to be
ignored. If any extraction/reduction products exist for such a spectrum
they will be deleted.

Modification History

97/12/11, Written by Marc W. Buie, Lowell Observatory
98/03/09, MWB, cleaned up logic needed when data are added to raw directory.
98/04/01, MWB, added some generalization items, and ADDPATH, DIRLIST
98/06, MWB, numerous changes to incorporate a numerical image profile for
the optimal extraction on the FINAL pass. Also added support
for those cases where more than one data directory can be found.
98/06/30, MWB, added user selection if data could be found in more than one
directory. Also, some logic was cleaned up that dealt with
spectra marked to be ignored.
98/08/25, MWB, changed the default plotting option, PLOTS=2 so that only
three windows are automatically created and used.
98/09/17, MWB, fixed a minor bookkeeping problem with 's' flagged frames.
The output files from these frames were still hanging around and
this has been changed so the output products are deleted.
99/11/24, MWB, changed lclxtrem call to accomodate new version.
2000/11/08, MWB, removed use of obsolete code constructs
2002/09/03, MWB, changed Str_sep call to strsplit
2003/10/01, MWB, converted to IDL file_mkdir calls