function corflag,datain,boardnum,pol,val=val,zero=zero,mask=mask,applymask=applymask
;program to interactively flag some bad data and remask with interpolated
;values. Data is returned to outdata, which is identical to the original
;data, in dimensions, parameters etc.... but without bad data!
;
;Data can be replaced with a specific value, which can be passed in with
;'val', or can be set to zero, indicated by the /zero switch. In the absence
;of these, the default is to make a linar interpolation (in the frequency
;direction only) across the band either side of the region to be
;flagged. The interpolation takes the mean of data which is located a
;distance equal to HALF THE SIZE OF THE FLAGGED REGION ON EITHER
;SIDE. i.e. for a flagged region across x1 to x2, data is interpolated from
;the mean of data from x0-(x1-x0)/2 to x1+(x1-x0)/2. There is some error
;checking for the available data for this, but not much, if you try to flag
;data too close to the edge of the band, or the flagged area is too large,
;it might barf.
;
;Some information is displayed on the screen plot, such as the x and y (for
;greyscale), otherwise it is x, y(x) for a plot. The value of the pixel at
;x,y or at y(x) is shown also.
;
;A mask of the flagged area (either a 1d or 2d set) can be returned by
;setting 'MASK'. This is helpful for later re-processing, or for doing
;repetitive masking. if usemask=mask is set, then the mask supplied in
;usemask is applied without going to the interactive stage. N.B. Applying an
;existing mask will only zero the data, or set it to a user-specified value,
;i.e. it does not determine an average in the way that the interactive
;approach does. To make it do this is time consuming and for me, not
;useful. Feel free to make the change if you wish.
;
;Note, this is a crappy script. It uses 'goto'. Sorry, I am too lazy to code
;it properly, I have data to reduce.. but now I can to it without
;interference spikes!!! yeah me.
;
;SYNTAX: OUTDATA=CORLFAG(DATA,BOARDNUM,POL,VAL=VAL,/ZERO,MASK=MASK,/APPLYMASK=APPLYMASK)
;        DATA - THE DATASET
;        BOARDNUM - SELECT THE BOARD TO FLAG
;        POL - CHOOSE THE POL TO FLAG (1,2)
;        VAL - THE VALUE WITH WHICH TO REPLACE FLAGGED DATA, THE DEFAULT IS
;              THE MEAN OF THE DATASET AROUND THE FLAGGED REGION.
;        ZERO - REPLACE FLAGGED DATA WITH ZEROS
;        MASK - SET THIS VARIABLE NAME, THE CREATED MASK IS RETURNED HERE.
;        APPLYMASK - PASS IN A PREVIOUSLY CREATED MASK HERE, THIS SKIPS THE
;                    INTERACTIVE PART AND JUST APPLIES THE MASK.
;EXAMPLE:
;TO DO A ONE-OFF, INTERACTIVE DESPIKE:
;despiked=corflag(spike_data,1,1)    ; this displays the first board and
;first polarisation of data 'spike' in an interactive plot, or greyscale for
;flagging. the flagged data is by default, set to an average. (use val=10 to replace
;to 10, or /zero to force it to zero). To do all boards and pols, it is
;necessary to do this recursively i.e.
;despiked=corflag(spike_data,1,1)
;despiked=corflag(despike_data,1,2)
;despiked=corflag(despike_data,2,1)
;despiked=corflag(despike_data,1,2)
;despiked=corflag(despike_data,3,1)
;despiked=corflag(despike_data,3,2)
;despiked=corflag(despike_data,4,1)
;despiked=corflag(despike_data,4,2)
;
;The flagging can be saved to a variable set by /mask. This variable is
;passed by reference OUT of the function and can be therefore used by sucessive
;iterations of CORFLAG.
;
;Once a mask has been created, it can be used for any other datasets,
;without the interaction with /applymask:
;despiked=corflag(spike,1,1,applymask=my_mask). 
;
;In this case, the setting of board and polarisation number are irrelevant,
;but must be valid numbers anyhow (I couldn't be bothered coding this in a
;more intelligent way just now).

data=datain
oldmulti=!p.multi
!p.multi=0
ans=strarr(1)   ; to get later queries from screen
!mouse.button=0
boardnum=boardnum-1  ; readjust these numbers for stupid IDL indexing
pol=pol-1

if boardnum+1 gt n_tags(data) or boardnum+1 le 0 then begin
    print,"That board number does not exist in this dataset"
    return,0
endif

datasize=size(data.(boardnum).d)
;Okay, so check for dimensions of data
;If there is three, then there the data probably is a series of spectra
;dumps, of each pol. If there is only two, then there is probably only two
;spectra, one for each pol. if there is one dimension, then it is only one
;spectra, and one pol.

case datasize(0) of  ; how many dimensions.. and how should it be displayed?
1:begin
npols=1
xsize=datasize(1)
ysize=1
if pol+1 gt npols or pol+1 le 0 then begin
    print,"There are not that number of pols for this data"
    print,strcompress(string(npols)+" pols detected")
    return,0
endif
im=data.(boardnum).d
dim=1
end

2:begin
npols=2
xsize=datasize(1)
ysize=1
if pol+1 gt npols or pol+1 le 0 then begin
    print,"There are not that number of pols for this data"
    print,strcompress(string(npols)+" pols detected")
    return,0
endif
im=data.(boardnum).d(*,pol)
dim=1
end

3:begin
npols=2
xsize=datasize(1)
ysize=datasize(3)
if pol+1 gt npols or pol+1 le 0 then begin
    print,"There are not that number of pols for this data"
    print,strcompress(string(npols)+" pols detected")
    return,0
endif
im=data.(boardnum).d(*,pol,*)
dim=2
end

else: begin
print,"The format for this data is not understood"
return,0
end
endcase


nbrds=n_tags(data)
;Ok, if the mask is supplied, apply it.,
if keyword_set(applymask) then begin
    if keyword_set(mask) then begin
      print,"Cannot create AND apply a mask."
      print,"Use mask=mask to create a mask first"
      return,0
    endif
    appmask_size=size(applymask.(boardnum)(*,*,pol))
    if appmask_size(0) eq 2 then mask_xsize=appmask_size(1)
    if total(size(data.(boardnum).d) eq size(applymask.(boardnum))) eq 0 $
      or n_tags(applymask) ne nbrds then begin
         print,"The mask has different dimensions to the dataset"
         return,0
     endif


if not keyword_set(val) then val=0.
for i=0,nbrds-1 do begin
data.(i).d=data.(i).d*(applymask.(i) eq 0)
data.(i).d=data.(i).d+val*applymask.(i)
print,strcompress(string(fix(total(applymask.(i))))+" pixels blanked.")
endfor
goto,stopping
endif

if n_tags(mask) eq 0 then begin
    print,"Creating new mask" 
    maskarray=0*im
    case nbrds of
        1:mask={b1:fltarr(xsize,npols,ysize)} 
        2:mask={b1:fltarr(xsize,npols,ysize),b1:fltarr(xsize,npols,ysize)}
        3:mask={b1:fltarr(xsize,npols,ysize),b2:fltarr(xsize,npols,ysize),b3:fltarr(xsize,npols,ysize)}
        4:mask={b1:fltarr(xsize,npols,ysize),b2:fltarr(xsize,npols,ysize),b3:fltarr(xsize,npols,ysize),b4:fltarr(xsize,npols,ysize)}
    endcase
endif else begin
    print,"modifying mask"
    if total(size(data.(boardnum).d) eq size(mask.(boardnum))) eq 0 then begin
        print,"Supplied mask and dataset dimensions do not match"
        return,0
    endif
    ;make a copy of the data, fill it with zeros for the mask
    if keyword_set(mask) then maskarray=0*im
endelse 

print,"Use the left or middle mouse buttons to define a region for changing"
print,"Click upper left hand corner first."
print,"Click the right hand mouse button to quit at any time."

;-Ok, now if the data has two dimensions, then greyscale it, otherwise,
;plot it.
if dim eq 2 then begin
remap:
!mouse.button=0
x=0
y=0
greyscale,im,max=maxim
oldposstr=strcompress("X:"+string(x)+" "+"Y: "+string(y))
oldval=strcompress("Value: "+string(im(x,y)))
xyouts,0.7,0.98,oldposstr,/norm
xyouts,0.2,0.98,oldval,/norm

maxim=max(im)


while !mouse.button eq 0 do begin
oldposstr=strcompress("X:"+string(x)+" "+"Y: "+string(y))
oldval=strcompress("Value: "+string(im(x,y)))
cursor,x,y,2,/data
if x lt 0 then x=0
if y lt 0 then y=0
if x ge xsize then x=xsize-1
if y ge ysize then y=ysize-1
newposstr=strcompress("X:"+string(x)+" "+"Y: "+string(y))
newval=strcompress("Value: "+string(im(x,y)))
xyouts,0.7,0.98,oldposstr,/norm,color=0
xyouts,0.2,0.98,oldval,/norm,color=0
xyouts,0.7,0.98,newposstr,/norm
xyouts,0.2,0.98,newval,/norm
endwhile

cursor,x0,y0,4,/data

if !mouse.button eq 4 then goto,stopping
if x0 lt 0 then x0=0
if y0 lt 0 then y0=0
if x0 gt xsize then x0=xsize-1
if y0 gt ysize then y0=ysize-1

polyfill,[x0,xsize-1,xsize-1,x0],[0,0,y0,y0],spacing=0.05,col=200

!mouse.button=0
while !mouse.button eq 0 do begin
oldposstr=newposstr
oldval=newval
cursor,x,y,2,/data
if x lt 0 then x=0
if y lt 0 then y=0
if x ge xsize then x=xsize-1
if y ge ysize then y=ysize-1
newposstr=strcompress("X:"+string(x)+" "+"Y: "+string(y))
newval=strcompress("Value: "+string(im(x,y)))
xyouts,0.7,0.98,oldposstr,/norm,color=0
xyouts,0.2,0.98,oldval,/norm,color=0
xyouts,0.7,0.98,newposstr,/norm
xyouts,0.2,0.98,newval,/norm
endwhile

if !mouse.button eq 4 then goto,stopping
cursor,x1,y1,4,/data

if x1 lt 0 then x1=0
if y1 lt 0 then y1=0
if x1 gt xsize then x1=xsize-1
if y1 gt ysize then y1=ysize-1
if x1 lt x0 or y1 gt y0 then begin
    print,"Must choose second click position inside shaded area"
     goto,remap
endif

greyscale,im
xyouts,0.7,0.98,newposstr,/norm
xyouts,0.2,0.98,newval,/norm
polyfill,[x0,x1,x1,x0],[y1,y1,y0,y0],spacing=0.05,col=200

if not(keyword_set(val)) and not(keyword_set(zero))then begin
    regionx=(x1-x0)/2.
    if x0-regionx lt 0 or x1+regionx gt xsize then begin
        print,"Region is too close to edge. Stopping"
        goto,stopping
    endif else begin
    width=(x1-x0)/2.
    lowside=mean(im(x0-width:x0,y1:y0))
    hiside=mean(im(x1:x1+width,y1:y0))
    val=(lowside+hiside)/2.
    endelse    
endif
if keyword_set(zero) then val=0

print,strcompress("Interpolate here? with "+string(val)+" [y/n]: ")
read,ans

while strlowcase(ans) ne 'y' and strlowcase(ans) ne 'n' do begin
    print,"Please confirm with 'y' or 'n'"
    print,"Interpolate here? [y/n]: "
    read,ans
endwhile

if strlowcase(ans) eq 'n' then begin 
goto,remap
endif

print,strcompress("Replacing "+strcompress(string(x0)+":"+string(x1),/remove_all)+$
" and "+strcompress(string(y0)+":"+string(y1),/remove_all)+" with "+string(val))
im(x0:x1,y1:y0)=val
val=0
if keyword_set(mask) then maskarray(x0:x1,y1:y0)=1
goto,remap
endif else begin  ; Ok, that was for a 2D display for greyscale, now if it is a spectrum....
;------------------------------------------

redraw:
!mouse.button=0
x=0
y=0
plot,im,yrange=[min(im),max(im)*1.1]
oldposstr=strcompress("X:"+string(x)+" "+"Y: "+string(im(x)))
xyouts,0.7,0.98,oldposstr,/norm
highlight=180

while !mouse.button eq 0 do begin
oldposstr=strcompress("X:"+string(x)+" "+"Y: "+string(im(x)))
cursor,x,y,2,/data
if x lt 0 then x=0
if y lt 0 then y=0
if x ge xsize then x=xsize-1
if y ge ysize then y=ysize-1
newposstr=strcompress("X:"+string(x)+" "+"Y: "+string(im(x)))
xyouts,0.7,0.98,oldposstr,/norm,color=0
xyouts,0.7,0.98,newposstr,/norm
endwhile

if !mouse.button eq 4 then goto,stopping
cursor,x0,y0,4,/data
if x0 lt 0 then x0=0
if x0 gt xsize-1 then x0=xsize-1
polyfill,[x0,x0,xsize-1,xsize-1],[min(im),max(im)*1.1,max(im)*1.1,min(im)],color=200,spacing=0.05
plot,im,yrange=[min(im),max(im)*1.1],/noerase

!mouse.button=0
while !mouse.button eq 0 do begin
oldposstr=strcompress("X:"+string(x)+" "+"Y: "+string(im(x)))
cursor,x,y,2,/data
if x lt 0 then x=0
if y lt 0 then y=0
if x ge xsize then x=xsize-1
if y ge ysize then y=ysize-1
newposstr=strcompress("X:"+string(x)+" "+"Y: "+string(im(x)))
xyouts,0.7,0.98,oldposstr,/norm,color=0
xyouts,0.7,0.98,newposstr,/norm
endwhile

if !mouse.button eq 4 then goto,stopping
cursor,x1,y1,4,/data
if x1 lt 0 then x1=0
if x1 gt xsize-1 then x1=xsize-1

if x1 lt x0 then begin
    print,"Must choose second click position inside shaded area"
     goto,redraw
endif

plot,im,yrange=[min(im),max(im)*1.1]
xyouts,0.7,0.98,newposstr,/norm
polyfill,[x0,x0,x1,x1],[min(im),max(im)*1.1,max(im)*1.1,min(im)],color=200,spacing=0.05
plot,im,yrange=[min(im),max(im)*1.1],/noerase


if not keyword_set(val) and not keyword_set(zero) then begin
    width=(x1-x0)/2.
    lowside=mean(im(x0-width:x0))
    hiside=mean(im(x1:x1+width))
    val=(lowside+hiside)/2.
 endif
if keyword_set(zero) then val=0
print,strcompress("Interpolate here with value "+string(val)+" ?")
read,ans

while strlowcase(ans) ne 'y' and strlowcase(ans) ne 'n' do begin
    print,"Please confirm with 'y' or 'n'"
    print,"Interpolate here? [y/n]: "
    read,ans
endwhile

if strlowcase(ans) eq 'n' then goto,redraw
im(x0:x1)=val
val=0
if keyword_set(mask) then maskarray(x0:x1)=1
goto,redraw

goto,stopping
endelse

stopping:
;finishing it all up.
if not keyword_set(applymask) then if npols eq 1 then data.(boardnum).d(*,*)=im else data.(boardnum).d(*,pol,*)=im
if keyword_set(mask) then begin 
    print,strcompress("Writing a mask with "+string(nbrds)+" boards")
    if dim eq 2 then if npols gt 1 then mask.(boardnum)[*,pol,*]=(maskarray) else  mask.(boardnum)[*,*]=fix(maskarray)
    if dim eq 1 then if npols gt 1 then mask.(boardnum)[*,pol]=(maskarray) else  mask.(boardnum)[*]=fix(maskarray)
endif
!p.multi=oldmulti
return,data

end