; SOURCE: beadtracker.tom     Author: Chris Renken
;
; PURPOSE:  Bead (Marker) tracker for SPIDER 

;<b>------------------- Edit next 3  Input parameters ----------------- 

x97 = 1                  ; First tilt file number
x90 = 31                 ; Zero tilt file number
x91 = 62                 ; Last tilt file number

x89 = 10                 ; Number of Markers
x80 = 8                  ; Marker diameter (pixels)
x88 = 1                  ; Density (1 light, 0 Dark)?

; ----------------------- Input files ---------------------------------

FR G
[in]rot_***              ; Tilted image file template              

FR G                                     
[mrk]d_rot***            ; Template for marker doc files

FR G
[ang]ang001              ; Tilt angle doc file 

; ---------------------- Output files --------------------------------------------

FR G                                     
[mrk]d_rot***            ; Template for marker doc files

; ----------------- END BATCH HEADER ------------------------------ </b>

x81 = x80/2
x82 = 1/x80
x24 = 0

FI x10,x11                    ; Get NSAM & NROW
[in]x90
(12,2)

;BEGIN THE MARKER SELECTION
DO LB12 j=1,2                 ; Divides into plus and minus branches
   x21 = 2*x0-3               ; Toggles between -1 and 1

   IF(x21.LT.0)THEN 
      x19 = x90-1             ; Number of images below reference
   ELSE
      x19 = x91-x90           ; Number of images above reference
   ENDIF

   x11 = x21+x90              ; 1st working image number
   x10 = x90                  ; Starting reference image number


   DO LB13 i=x97,x19          ; Specifles File number

      UD x11,x23,x40          ; Get tilt angle
      [ang]

      SD -1,x24,x40,x24       ; Write tilt angle into marker file
      [mrk]x11

      ;Accentuate markers in the current image
      FQ
      [in]x11
      _4 
      (1)
      x82

      ;Accentuate markers in the refence file      
      FQ
      [in]x10
      _3 
      (1)
      x82

      ; BEGIN SEARCHING FOR ALL MARKERS ON AN IMAGE
      DO LB14 x20=1,x89          ; Specify marker number
         UD x20,x13,x14          ; GET MARKER COORDINATES
         [mrk]x10

         x15 = x13-25            ; TOP-LEFT X COORDINATE FOR WINDOWING
         x16 = x14-25            ; TOP-LEFT Y COORDINATE FOR WINDOWING

         ; WINDOW THE REFERENCE IMAGE
         WI
         _3 
         _2
         (50,50)
         (x15,x16)

         ; WINDOW THE WORKING IMAGE
         WI
         _4
         _1
         (50,50)
         (x15,x16)

         ; CROSS-CORRELATE THE WINDOWED IMAGES
         CC
         _1
         _2
         _5

         ; DETERMINE THE RELATIVE SHIFT
         PK M x45,x46,x47,x48,x49
         _5

         ; Keep Blank
         IF (x88.EQ.0) THEN
            NEG
            _1
            _9
            GOTO LB10 
         ENDIF

         CP
         _1
         _9

         LB10

         MA                 ; Mask
         _9
         _2
         x81
         D
         A
         x45,x46

         PK M x45,x46,x47,x48,x49
         _2

         ; Keep Blank
         ;UPDATE THE MARKER COORDINATES
         x17 = x47+x13
         x18 = x48+x14

         ; SAVE TO THE NEW MARKER FILE
         SD x20,x17,x18
         [mrk]x11

      LB14

      x10 = x11         ; WORKING IMAGE BECOMES NEW REFERENCE
      x11 = x11 + x21     ; WORKING IMAGE UPDATED
   LB13

   x97 = 1

LB12

EN