vp_art
======

A suite of scripts designed to reduce data from the VIRUS-P spectrograph in an autonomous fashion.


(0a)  Indicators for reduction steps

        b = bias subtracted
        t = trace aligned
        c = cosmic rays removed
        s = sky subtracted


(0b) This code is based in python and requires these imports.
     Version numbers are included where possible and are the
     versions upon which the code was written and tested.
        os
	glob
	numpy --- 1.5.1
	scipy --- 0.8.0
	pyfits --- 2.4.0
	shutil
	matplotlib --- 1.0.1
	subprocess
	astLib --- 0.4.0



(1)  first the directory order...

         working_dir/  --->  raw/  --->  20120920/  20120921/  20120922/

     ...the date-directories must be "yyyymmdd"
     The working_dir must have the file "TARGETS.list" which lists all the
     the observed targets (with coordinates) over all nights.
     It must have this format...

     # name  ra  dec
     object1  hh:mm:ss.s  (+-)dd:mm:ss.s
     object2  hh:mm:ss.s  (+-)dd:mm:ss.s
     ...

(2)  Run the setup script with "python vp_art_setup.py"
     It creates the appropriate directory structure...

     working_dir/redux/  --->  20120920/  20120921/  20120922/

     working_dir/redux/20120920/calib/
     working_dir/redux/20120920/calib/bias/
     working_dir/redux/20120920/calib/comp/
     working_dir/redux/20120920/calib/flat/

     working_dir/redux/20120920/object/
     working_dir/redux/20120920/object/name1/
     working_dir/redux/20120920/object/name2/

     ###  where name* is the object name from the FIELDS.list
     ###  NOTE: Only the targets listed in FIELDS.list will
     ###        be considered. Others will be ignored.

(3)  Run the reduction script with "python vp_art_reduce.py"

(a)  Step 1 is to make master stacks
    --> BIAS_COMBINE   y       #  Create master bias stack
    --> COMP_COMBINE   y       #  Create master comp stack
    --> FLAT_COMBINE   y       #  Create master flat stack


(b)  Step 2 is to do bias-subtraction
    --> BIAS_SUBTRACT  y       #  Perform bias subtraction

(c)  Step 3 is to trace fibers. First, fibers are found from the
     first column (leftmost) of the flat-stack and trace (rightwards).
     Next, trace-aligning is performed where the curvature of each
     fiber is removed, essenially "flattening" them horizontally.
    --> FIBER_TRACE    y       #  Trace fibers 

(d)  Step 4 is to calculate the wavelength solution. For this you'll
     need a data file indicating locations of lines in the comp-lamp
     data. 





FLAT-FIELDING

since we dont have "appropriate" calibration flats, we have to improvise
a flat-fielding routine... here it is.

(0) This routine requires these inputs...
    - A master twiflat for the night
    - An observation of a standardized target (standard star)
    - The spectrum of the standardized target

PROCESS

(1) Basic reductions are run on the standard.

(2) From "vp_art.param" the highest S/N fiber for each image
is selected from the specified fiber-range. For example, if
STD_RANGE=45,64 then the highest S/N fiber between fibers 45
and 64 will be assumed to be the standard target.

(3) These selected spectra are then median-combined (to remove
cosmic rays) into a master standard.

(4) This master is divided by the input standard spectrum to
extract the flat-field (for the fiber).

	FLATFIELD_x = (MEASURED SPECTRUM) / (KNOWN SPECTRUM)

(5) This flat-field is extended to other fibers using the master
twiflat. Since S/N is very high for each fiber in the twiflat,