A number of command line image processing routines have been established.

Build a FITS image from scratch.  
Usage:  clip_build_fits.sh 775 771 d.1 a.fits 
arg1 - X dimension of image to be made (= NAXIS1). 
arg2 - Y dimension of image to be made (= NAXIS2). 
arg3 - polynomial coefficients file (bgnmp-style) 
arg4 - name of output fits file 
N.B. If PolyFile is not present, Zero image is made. 


Numerically map (and subtract) the background of an image.  
Usage:  clip_bgnmp.sh a.fits clip_pixseq.out 14 
arg1 - input FITS image 1
arg2 - XYZ pixel file (from clip_pixseq.sh) 
arg3 - number of polynomial coefficients  


Refine target centers in an image. 
Usage:  clip_boxcen.sh a.fits listIN 10.0 0 listOUT
arg1 - input FITS image 1
arg2 - input file of X,Y 
arg3 - search radius in pixels    (float)  
arg4 - centering radius in pixels (int)    
arg5 - output file of X,Y 


Use fiber (flat) peaks to integrate signal 
Usage: clip_fibsigx.sh a.fits peaks.txt 528 2   
arg1 - input FITS image 
arg2 - peaks file (from peaks.sh) 
arg3 - fixed X (column) that peak file corresponds to 
arg4 - integration window radius in X 


Locate spectra in VIRUS flat 
Usage: Usage:  clip_fibsx.sh a.fits 528 2 none  
arg1 - input FITS image 
arg2 - fixed X (column) for search 
arg3 - smoothing radius in X 
arg4 - output image name (none for no image) 


Perform image arithmetic. 
Usage:  clip_imarith.sh a.fits - b.fits o.fits 
arg1 - input FITS image 1
arg2 - operation (-,+,/,*) 
arg3 - input FITS image 2 
arg4 - output image name 
Note: You can also used constants:
Usage:  clip_imarith.sh 2000.0 / b.fits o.fits 


Apply X,Y shifts to an image.  
Usage:  clip_imshift_2term.sh a.fits 12.33 -1.33 out.fits
arg1 - input FITS image (to be shifted)
arg2 - X shift (pixel units) 
arg3 - Y shift (pixel units) 
arg4 - Output (shifted) FITS image name 


Compute image statistics.  
Usage:  clip_imstat.sh a.fits 50 100 100 300
arg1 - input FITS image 1
arg2 - min i of image sub-region 
arg3 - max i of image sub-region 
arg4 - min j of image sub-region 
arg5 - max j of image sub-region 
Note: Use 0 0 0 0 for entire image 


Gather pixel values (x,y,i) from an image.  
Usage:  clip_pixseq.sh a.fits 1500 50 100 100 300
arg1 - input FITS image 1
arg2 - number of pixels to be gathered 
arg3 - min i of image sub-region 
arg4 - max i of image sub-region 
arg5 - min j of image sub-region 
arg6 - max j of image sub-region 


Smooth an image. 
Usage:  clip_smooth_rbox.sh a.fits 2 mean o.fits
arg1 - input FITS image
arg2 - box smoothing radius (pixels) 
arg3 - method (mean,median) 
arg4 - output image name 


Combine (stack) multiple images.
Usage:  clip_stacker.sh list1 mean result.fits
arg1 - list of input FITS images
arg2 - method (mean,median)
arg3 - Output (shifted) FITS image name 


Threshold image in a min,max range. 
Usage:  clip_threshpat.sh a.fits 0.0 10000.0 o.fits
arg1 - input FITS image
arg2 - low (min) threshold value
arg3 - high (max) threshold value
arg4 - output image name 



Mirror flip an image. 
Usage:  clip_flip.sh a.fits X o.fits 
arg1 - input FITS image
arg2 - flip sense (X,Y)
arg3 - output image name 


Collapse image along Column or Row. 
Usage:  clip_collapse.sh a.fits Y 2 o.fits 
arg1 - input FITS image
arg2 - collapse sense (X for column average, Y for row average)
arg3 - number of row/col to average (2)  
arg4 - output image name 


Derive X,Y shifts between two images. 
Usage:  clip_xy2xy_2term.sh img1.fits img2.fits 
arg1 - base FITS image 
arg2 - FITS image to be to transformed (to base)



 
 
Higher level scripts: 

View image and mark X,Y of sources. 
Usage: Usage: ds9_set_xy a.fits 6.0 20 3 
arg1 - input FITS image name 
arg2 - sigma-level for image scaling 
arg3 - search radius in pixels  
arg4 - centering radius (Integer,pixels)  


Register and stack a list of images. 
Usage: small_shifts_stacker list1 8.0 20 3  
arg1 = filename for list of FITS images
arg2 - sigma-level for image (display) scaling
arg3 - search radius in pixels
arg4 - centering radius (Integer,pixels)