;+
; NAME: autoregister
; PURPOSE:
; 	Automagically register a bunch of images.
;
;USAGE:
; 	This accepts either an image stack datacube or an array of pointers to 
; 	images, and registers and mosaics them together via cross correlation.
; 	This is mostly just a convenient driver function for subreg and mosf,
; 	in other words. 
;
; INPUTS:
; 		array	either an array of images, or a ptrarray pointing to
; 				a bunch of images of different size. if the latter,
; 				autoregister pads as necessary, then registers.
; KEYWORDS:
; 		/nantozero	set NaNs to 0 before registering. This saves a lot of time
; 					versus running fixpix in subreg.
;		/justpad	Given an ptrarry, just pad them and concatenate into
;					one variable, returned as 'padded'
;
;		padded=		output variable for padded array
;		mosaic= 	output variable for the mosaiced sum
;
;		shifts=		use these shifts instead of registering
;
; 		use _extra to pass keywords to subreg or mosf.
; 		
; OUTPUTS:
;
; HISTORY:
; 	Began 2005-04-08 00:33:48 by Marshall Perrin 
; 	2005-06-30: Subpixel registration now the default
; 	2006-04-27: Can now pass shifts in as an argument
;-
PRO autoregister,array,arrayout,expmap=expmap,_extra=_extra,refimage=refimage,$
	nantozero=nantozero,mosaic=mosaic,exptimes=exptimes,padded=ar,justpad=justpad,$
	subpixel=subpixel,shifts=shifts,px=px,py=py


	if n_elements(subpixel) eq 0 then subpixel =1  ; default is now subpixel

	if size(array,/type) eq 10 then begin
		message,/info,"Passed an array of pointers to images; padding as needed."
		ni = n_elements(array)
		sizes = fltarr(6,ni)
		for i=0,ni-1 do sizes[0,i] = size(*array[i])

		ar = fltarr(max(sizes[1,*]),max(sizes[2,*]),ni)+!values.f_nan
		for i=0,ni-1 do ar[0:sizes[1,i]-1,0:sizes[2,i]-1,i] = *array[i]
	endif else begin
		ar = array
	endelse

	if keyword_set(justpad) then return

	if keyword_set(nantozero) then begin
		wnan = where(~finite(ar),nanct)
		masks = finite(ar)
		if nanct gt 0 then ar[wnan]=0
	endif
	if ~(keyword_set(refimage)) then refimage = 0
	if ~(keyword_set(shifts)) and ~(keyword_set(px)) and ~(keyword_set(py)) then subreg,ar[*,*,refimage],ar,shifts,_extra=_extra
	
	;plot,shifts[0,*],shifts[1,*],psym=-2
	;stop
	
	; use PX and PY if they're passed in.
	if ~keyword_set(px) or ~keyword_set(py) then begin
		subreg_shiftstopeaks,ar,shifts,px,py,ref=ar[*,*,refimage]
	endif
	mosf,ar,px,py,mosaic,expmap,pieces=arrayout,exptimes=exptimes,subpixel=subpixel,$
		masks=masks,_extra=_extra


end