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MIKE Pipeline Optional Arguments and Stuff

Greg Walth's Brief Listing of Arguments for mikesetup

Misc. documentation items:

-d DATADIRdirectory of data
-db DBNAMEname

-2D*generates 2D spectra, and simple (non-GHLB) 1D extractions
-allgenerates pipelines for all targets
-blueoption generates pipelines for blue frames
-date DATEoption generates pipelines for specific date
-db DATABASEdatabase file
-dkx FLOATset non-standard knot spacing for skysub
-flatblue FLATBLUElocation to a specific flatblue frame
-flatkey FLATSTRINGstring to search for flat frames in database file
-flatred FLATREDlocation to a specific flatred frame
-fringe FRINGElocation to a specific fringe frame
-fringekey FRINGESTRINGstring to search for fringe frames in database file
-ignoresets ignore string
-individualseparate extractions
-lampblue LAMPBLUElocation to a specific lampblue frame
-lampkey LAMPSTRINGstring to search for lamp frames in database file
-lampred LAMPREDlocation to a specific lampred frame
-logboption bins extracted spectra logarithmically in wavelength
-mk MAKEFILEcreates a makefile for multiple targets
-nofakedo not make model spectra (less time to run)
-noobjects(a) Compute sky masks instead of sky apertures; construct wide/dummy extraction apertures, and in 2D mode do not extract 1D spectra
-noskyapsDo not compute sky apertures or masks
-noslitfnoption skips the generation and usage of a slit function
-onlyflatOnly generate the flatfield pipelines
-onlylampOnly generate the comparison lamp pipelines
-orderkey ORDERSTRINGstring to search for order frames in database file
-orderspanOptional comma-separated pair of column coordinates to specify portion of data frames to be reduced (e.g. To reduce the reddest 500 columns, use "-orderspan 0,500")
-redoption generates pipelines for red frames
-rnRead noise, in electrons, if the header values are not to be used
-skykeyString to identify science frames to be used as sky frames
-skyshiftUse sky lines to compute zero-point shifts in the red wavelength solutions [unstable]
-slitblue SLITBLUElocation to a specific slitblue frame
-slitred SLITREDlocation to a specific slitred frame

* option is experimental

science frames
file extensions descriptions
f divided bv flatfield
ff divided by flatfield and fringe frame; i.e. red only, and optional
s divided by slit-function
m model of sky
o (object) model of sky has been subtracted
p fake frame, GHLB fit to o
lamp frames
file extensions descriptions
f divided flatfielded
s divided slitfunction
b spacial filtered to isolated th ar lines
_scat generated during spacial filtering (temp) not useful
x-rect frame containing rect transforms (line curvature)
specs 1d extracted th ar spectra for each order used for wavelength cal.
diagnostic files
files descriptions
blaze{blue,red}.fits flatened quartz spectrum
flat{blue,red}.fits pixel to pixel flat
mask{blue,red}.fits mask image for excluding pixels for analysis
slit{blue,red}.fits slit-function
slit{blue,red}-y-dist.fits y-distortion (order curvature) from the quartz
unknown files
files descriptions
actual.fits ???
ccsum.fits ???
fitted.fits ???
flat1d.fits ???
lc.fits ???
lowmask.fits ???
refer.fits ???
refspecs.fits ???
spatial.fits ???
udata.fits ???
uflatdata.fits ???
files that get over-written
files descriptions
p.fits profile of the slit-function and profile of the lamp
CT.fits cross-correlation of the profiles of the slit-function and the lamp
found.dat generated wavelength cal.
knots.dat generated sky-subtraction
What are the parameters for:
  • getrect
  • GHLBExtract