; SOURCE: ivem2spi.tom                               2/11/03  M. Marko
; Changes: 1/18/05  Added CE VS command and changed default thresh.jl 
;
; PURPOSE: Converts tilt-series files from the JEOL 4000 to SPIDER format
;
; Input  (typical):     1024x1024 16-bit raw files recorded using
;                       Emispec autosave. 
;                            
; Output (typical):     SPIDER images: CCD defects removed, 
;                       rotated to make tilt axis vertical,
;                       padded to avoid wrapping after rotation.
;
; NOTE 1: If you want to check that the threshold for outlyers due
;         to CCD defects is not cutting off any data, convert a test 
;         image to SPIDER and use 'HI R' with the threshold you plan to 
;         use for the series.  For typical cryo images with a mean
;         below 1000, a threshold of 1500 is generous.
;
; NOTE 2: Column defects appear to be at x=423 and 424.  If lines are
;         still seen in the output images, these positions might need 
;         to be modified.  If blooming occurs, more lines may need to
;         be filled in.
;
; NOTE 3: Images are automatically padded according to the angle of
;         the tilt axis from vertical.  This avoids cutting off the
;         corners of rotated images.  This procedure is only
;         implemented for square images of 1024x1024 pixels.
;

x11 = 1                ; First image file number (usually 1)
x12 = 122              ; Last image file number  (usually 61 or 122)

x99 = 1500             ; Threshold for outlying pixels (usually 1500,7000)
x97 = 3                ; Box size for CE VS. 0 = no filter,3,5,7
x98 = 0                ; Rotation angle for vertical tilt axis

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

FR G                                     
[input]rawinput/raw_            ; Raw input image filename prefix (adds ###)

; ----------------- Output files ----------------------------
FR L
[warning]ChangedImagePixels     ; File retains # of pixels changed by CE VS
FR G
[output]rotated/rot_            ; Rotated windowed output prefix (adds ###)

; ----------------- END BATCH HEADER ----------------------
x42 =0  ;flag for one time warning of CE VS
; For 1024x1024 Tietz images 
x30 = 1024               ; Input size

; ------ Convert from raw to SPIDER, adding leading zeros

DO LB1 x13=x11,x12
   IF (x13.LT.10) THEN   ; Convert binary filenames to SPIDER convention
      VM
      \cp [input]{*x13}.bin jnk_tmp.$DATEXT
   ELSE
      IF (x13.LT.100) THEN 
         VM
         \cp [input]{**x13}.bin jnk_tmp.$DATEXT
      ELSE
         VM
         \cp [input]{***x13}.bin jnk_tmp.$DATEXT
      ENDIF
   ENDIF

   CP FROM RAW          ; Convert image to SPIDER format
   jnk_tmp              ; Raw input images  filename   (input)
   (16)                 ; 16 Bits in image file format                    
   (x30,x30)            ; Size
   (0)                  ; Header offset 
   (2)                  ; Endedness 
   N                    ; Do not fold negatives
   _1                   ; Temp. file                   (output)

   ;-------- Remove column defect lines by replacing with adjacent

   WI
   _1                   ; SPIDER image                 (input)
   _2                   ; Windowed line                (output)
   (1,x30)              ; Window size
   (423,1)              ; Window position

   IN                   ; Put adjacent window in image
   _2                   ; Windowed line                (output)
   _1                   ; SPIDER image                 (input)
   (424,1)              ; Position


   WI
   _1                   ; SPIDER image                 (input)
   _2                   ; Windowed line                (output)
   (1,x30)              ; Window size
   (426,1)              ; Window position

   IN                   ; Put adjacent window in image
   _2                   ; Windowed line                (input)
   _1                   ; SPIDER image                 (output)
   (426,1)              ; Position

   ;------- Remove bright outlyers due to single-pixel defects
   TH
   _1                   ; SPIDER image                   (input)
   _2                   ; Thresholded SPIDER image       (output)
   A
   x99                  ; Thresholded level
   
  ;----added CE VS operation
  IF(x97.GT.1)THEN
    x41=0
    CE VS x41
    _2     ;input
    _3     ;output
    (x97,x97)
    
    ;---changed pixels?
    IF(x41.GT.0)THEN
      
      ;---one time warning
      IF(x42.EQ.0)THEN
        VM
        echo "CE VS has changed pixels, read [warning] "
      
        SD /key=image# reg1= #pixels changed
        [warning]
      
        x42=3
      ENDIF
      
      ;---print # of change pixels if any
      SD x13,x41
      [warning]
      
    ENDIF
  
    cp
    _3
    _2
  ENDIF
       
  ;------- In case rotation is zero or ninety degrees
  x22=ABS(x98)
  IF (x98.EQ.0) THEN
      CP                   ; Rotation is zero degrees
      _2                   ; Thresholded SPIDER image       (input)
      [output]{***x13}

  ELSE 
      IF (x22.EQ.90) THEN
         RT                   ; Rotation is ninety degrees
         _2                   ; Thresholded SPIDER image    (input)
         [output]{***x13}     ; Rotated, thresholded image  (output)        
         x98                  ; Angle

      ELSE
         ; Calculate size for padding based on tilt axis angle
         x23 = ABS(x22-45)
         x24 = 1.414*cos(x23)
         x25 = x24*1024       ; padded image dimension
         x26 = (x25-1024)/2   ; top left coordinate

         PD                   ; Pad so rotation won't lose corners
         _2                   ; Thresholded SPIDER image    (input)
         _1
         (x25,x25)            ; Padded image dimension
         M
         (x26,x26)            ; Top left coordinate

         RT M                 ; Rotate so tilt axis is vertical
         _1
         [output]{***x13}     ; Rotated, thresholded image  (output)        
         x98
      ENDIF
   ENDIF

   FS
   [output]{***x13}     ; Rotated, thresholded image        (output)        
LB1

; Clean up temp files
DE
_1
DE  
_2
DE
jnk_tmp.jnk

EN