;+
; NAME:
;  goodpoly
; PURPOSE: (one line)
;  Robust fitting of a polynomial to data.
; DESCRIPTION:
;  This is a multi-pass fitting routine that fits a fixed order polynomial
;  to the input data.  After each pass, the scatter of the fit relative
;  to the fitted line is computed.  Each point is examined to see if it
;  falls beyond THRESH sigma from the line.  If is does, it is removed
;  from the data and the fit is tried again.  This will make up to two
;  attempts to remove bad data.
; CATEGORY:
;  Function fitting
; CALLING SEQUENCE:
;  coeff = goodpoly(x,y,order,thresh,yfit,newx,newy)
; INPUTS:
;  x      - Input dataset, independant values.
;  y      - Input dataset, dependant values.
;  order  - Order of the polynomial fit (linear = 1).
;  thresh - Sigma threshold for removing outliers.
; OPTIONAL INPUT PARAMETERS:
; KEYWORD PARAMETERS:
;  BAD     - Vector of flags, same length as x and y, that indicate bad values
;              in the y vector.  The default is that all points are considered
;              good at the stars.  If supplied, any additional bad values found
;              will be marked as bad in this vector upon output.  Also, any
;              NaN values found in either the x or y vector will be trimmed
;              from the data (and marked bad) prior to any processing.
;  EXCLUDE - Number of points to exclude from initial pass fit.  This number
;              is rounded up to the next even number.  Then EXCLUDE/2 of the
;              highest and lowest points are removed before the first fit.
;              If these numbers are reasonable, they will not be excluded
;              in the second pass.  This helps prevent biasing the first fit
;              with the worst points in the array.  Default is to not exclude
;              any points on the first pass.
;  MAX_VALUE - The maximum value to be fitted.  If this keyword is provided,
;                data values greater than MAX_VALUE are treated as missing
;                and are not used in the fit at any pass.
;  MIN_VALUE - The minimum value to be fitted.  If this keyword is provided,
;                data values greater than MIN_VALUE are treated as missing
;                and are not used in the fit at any pass.
;  SIGMA   - Standard deviation of difference between good points and the
;              fitted curve.
; OUTPUTS:
;  yfit   - Fitted values for y that match the input vector.
;  newx   - X values from input that were considered good.
;  newy   - Y values from input that were considered good.
;  Return value is the set of polynomial coefficients.
; COMMON BLOCKS:
; SIDE EFFECTS:
; RESTRICTIONS:
; PROCEDURE:
; MODIFICATION HISTORY:
;  Written 1991 Feb., Marc W. Buie, Lowell Observatory
;  93/11/12, MWB, Program fixed to return a computed y for all input x.
;  95/09/20, MWB, Added EXCLUDE keyword.
;  98/02/09, MWB, Added SIGMA keyword.
;  98/06/08, MWB, Added MIN/MAX_VALUE keywords.
;  98/08/12, MWB, Revamped some logic plus added direct support for badflags.
;                    The new version is probably a tad faster and more robust
;                    than the old version.
;-
function goodpoly,x,y,order,thresh,yfit,newx,newy, $
            EXCLUDE=exclude,SIGMA=sigma,BAD=bad, $
            MIN_VALUE=min_value,MAX_VALUE=max_value

if badpar(exclude,  [0,1,2,3],    0,CALLER='goodpoly (EXCLUDE) ', $
                                    DEFAULT=0) then return,0
if badpar(min_value,[0,1,2,3,4,5],0,CALLER='goodpoly (MIN_VALUE) ', $
                                    type=minvtype) then return,0
if badpar(max_value,[0,1,2,3,4,5],0,CALLER='goodpoly (MAX_VALUE) ', $
                                    type=maxvtype) then return,0

savebad = n_elements(bad) eq n_elements(y)

xx = x
yy = y
arlen=n_elements(xx)
;print,'arlen at start',arlen,total(bad)

; Take note of all points that start out good for later indexing into the
;   input bad array.  Also weed out the points that are known bad at the start.
if savebad then begin
   z = where(bad eq 0,count)
   IF count ne 0 and count ne arlen THEN BEGIN
      xx = xx[z]
      yy = yy[z]
   ENDIF ELSE IF count eq 0 THEN BEGIN
      print,'GOODPOLY: Error! All values are marked bad, nothing to fit.'
      coeff=fltarr(order+1)
      coeff[0]=0.0
      return,coeff
   ENDIF
   ; Save the indicies into the original array for all the good points.
   ;   This will be needed later if any points are marked bad.  This array
   ;   should maintain the same length as the xx,yy arrays but will point
   ;   back into the original arrays, x,y,bad
   goodidx = z
endif
arlen=n_elements(xx)

; Filter out any NaNs
z = where(finite(xx) eq 0 or finite(yy) eq 0,count)
if count ne 0 and count ne arlen then begin
   if savebad then bad[goodidx[z]]=1
   z = where(finite(xx) eq 1 and finite(yy) eq 1)
   xx = xx[z]
   yy = yy[z]
   if savebad then goodidx = goodidx[z]
endif else if count eq arlen then begin
   print,'GOODPOLY: Error! All values are either NaNs or marked bad, nothing to fit.'
   coeff=fltarr(order+1)
   coeff[0]=0.0
   return,coeff
endif
arlen=n_elements(xx)

; Need an inverted bad flag array for further processing.
if savebad then gflag = 1B-bad

; If min_value provide, exclude those values now
IF minvtype ne 0 THEN BEGIN
   z = where(yy gt min_value,count)
   IF count ne 0 and count ne arlen THEN BEGIN
      xx = xx[z]
      yy = yy[z]
      if savebad then begin
         gflag[goodidx[z]]=gflag[goodidx[z]]*2B
         gflag = gflag/2B
         goodidx = goodidx[z]
      endif
   ENDIF ELSE IF count eq 0 THEN BEGIN
      print,'GOODPOLY: Error! All y values are below min_value, nothing to fit.'
      coeff=fltarr(order+1)
      coeff[0]=min_value
      return,coeff
   ENDIF
ENDIF
arlen=n_elements(xx)

; If max_value provide, exclude those values now
IF maxvtype ne 0 THEN BEGIN
   z = where(yy lt max_value,count)
   IF count ne 0 and count ne arlen THEN BEGIN
      xx = xx[z]
      yy = yy[z]
      if savebad then begin
         gflag[goodidx[z]]=gflag[goodidx[z]]*2B
         gflag = gflag/2B
         goodidx = goodidx[z]
      endif
   ENDIF ELSE IF count eq 0 THEN BEGIN
      print,'GOODPOLY: Error! All y values are above max_value, nothing to fit.'
      coeff=fltarr(order+1)
      coeff[0]=max_value
      return,coeff
   ENDIF
ENDIF
arlen=n_elements(xx)

; Initial fit with all the data.
if exclude eq 0 or arlen le (exclude+order) then begin
   coeff=poly_fit(xx,yy,order,yfit)
;   chisq0=total((yy-yfit)^2)/(arlen-order)  
   flat = (yy-yfit)+(total(yfit)/arlen)
   sigma = stdev(flat,mean)
 
; Initial fit excluding EXCLUDE extrema points before fit.
endif else begin
   nex = ceil(exclude/2.0)
   sidx=sort(yy)
   sidx=sidx[nex:arlen-1-nex]
   coeff=poly_fit(xx[sidx],yy[sidx],order)
   yfit = poly(xx,coeff)
;   chisq0=total((yy-yfit)^2)/(arlen-order)  
   flat = (yy-yfit)+(total(yfit)/arlen)
   sigma = stdev(flat[sidx],mean)
endelse

;Remove all points beyond threshold sigma
good=where( abs(flat-mean) lt thresh*sigma,goodnum)
nbad = arlen-goodnum 
if goodnum ne 0 and goodnum ne arlen then begin
   xx=xx[good]
   yy=yy[good]
   if savebad then begin
      gflag[goodidx[good]]=gflag[goodidx[good]]*2B
      gflag = gflag/2B
      goodidx = goodidx[good]
   endif
   arlen=goodnum
endif
 
if nbad ne 0 then begin

   ; Second pass fit with bad points removed (if needed).
   coeff=poly_fit(xx,yy,order,yfit)
;   chisq1=total((yy-yfit)^2)/(arlen-order)  
   flat = (yy-yfit)+(total(yfit)/arlen) 
   sigma = stdev(flat,mean)
 
   ;Remove all points beyond threshold sigma
   good=where( abs(flat-mean) lt thresh*sigma,goodnum)
   nbad = arlen-goodnum 

   if goodnum ne 0 and goodnum ne arlen then begin
      xx=xx[good]
      yy=yy[good]
      if savebad then begin
         gflag[goodidx[good]]=gflag[goodidx[good]]*2B
         gflag = gflag/2B
         goodidx = goodidx[good]
      endif
      arlen=goodnum
   endif
endif

; Third pass fit with bad points removed.
if nbad ne 0 then begin
   coeff=poly_fit(xx,yy,order,yfit)
;   chisq2=total((yy-yfit)^2)/(arlen-order)
   flat = (yy-yfit)+(total(yfit)/arlen)
   sigma = stdev(flat,mean)
endif

newx=xx
newy=yy

yfit = poly(x,coeff)
if savebad then bad = 1B - gflag

return,coeff

end