; Tests some SPIDER enhancement filters which require a 
; threshold setting with different input parameters on a volume.
; Places a single relevant slice from the volume in a stack.
; 
; ArDean Leith   April 2002     (INDEXED)
;
; ----------------------------------- GET INPUT PARAMETERS
FR
?input volume name? <1>
;nik000     

FR
?output stack name? <2>
;jnkstk     

; One relevant slice from your volume to be displayed
RR x40
?Enter relevant slice?
;x40=41     

RR x88
?Threshold?
;x88= 0.05  

; ----------------------------------- INITIALIZATION

PS Z       ; Extract relevant slice
<1>        ; Input volume
_9         ; Output slice
(x40)      ; Slice number

FS X32,x31
<1>        ; Temp volume
FS X42,x41
_9         ; Output slice

x11=99

; ----------------------------------- Original Unfiltered Slice
CP         ; Extract relevant slice
_9         ; Output slice
<2>@{***x11}; Output stack
VM 
echo "Image: {***x11} Original Unfiltered Slice"
x11=x11+1  ; Increment stack pointer

; ----------------------------------- CE -- Stretch Single

x12 = x41 + 0.1 * (X42 - x41)
x13 = x42 - 0.1 * (X42 - x41)

CE          ; CE
_9          ; Input image
<2>@{***X11} ; Output stack
S           ; Stretch
Single      ; Single mapping
X12
x13

VM 
echo "Slice: {***x11} CE S S 10..90%"
x11=x11+1  ; Increment stack pointer


; ----------------------------------- CE -- Histogram Equalization

CE          ; CE
_9          ; Input image
<2>@{***X11} ; Output stack
H           ; Histogram Equalization
N           ; No print
VM 
echo "Slice: {***x11} CE H"
x11=x11+1  ; Increment stack pointer

; ----------------------------------- CE -- Local Histogram Equal.
DO LB2 X21=6,11
   x22 = x21 * 2 + 1

   CE          ; CE
   _9          ; Input image
   <2>@{***X11} ; Output stack
   L           ; Local Histogram
   G           ; Generalized Stretch
   x22         ; Local Area Size

   VM
   echo "Slice: {***x11} CE L Generalized Size: {***x22}"
   x11=x11+1   ; Increment stack pointer
LB2

; ----------------------------------- CE -- Local Histogram Equal.
DO LB3 X21=1,5
   x22 = x21 * 10

   CE          ; CE
   _9          ; Input image
   <2>@{***X11} ; Output stack
   L           ; Local Histogram
   T           ; Threshold Stretch
   (x22)       ; Threshold

   VM
   echo "Slice: {***x11} CE L  Threshold: {***x22}"
   x11=x11+1   ; Increment stack pointer
LB3

GOTO LB99
; skip due to allocation problems
; ----------------------------------- ER EDM DIStance Map

   ER EDM       ; CE
   <1>          ; Input Volume
   _1           ; Output Volume
   x88          ; Threshold

   PS Z         ; Extract relevant slice
   _1           ; Temp volume
   <2>@{***x11} ; Output stack
   (x40)        ; Slice number

   VM
   echo "Slice: {***x11} ER EDM  At Threshold"
   x11=x11+1   ; Increment stack pointer

LB99

; ----------------------------------- FC

   FC           ; FC
   _9           ; Input Image
   <2>@{***X11}  ; Output stack
   3            ; Number of Contours
   NO           ; No overwrite

   VM
   echo "Slice: {***x11} FC "
   x11=x11+1   ; Increment stack pointer

; ----------------------------------- FC E

   FC E         ; FC E
   _9           ; Input Image
   <2>@{***X11}  ; Output stack
   X88          ; Bottom Contour
   10000        ; Increment
   NO           ; No overwrite

   VM
   echo "Slice: {***x11} FC E at Threshold "
   x11=x11+1   ; Increment stack pointer

; ----------------------------------- TH F

   TH F         ; THF
   _9           ; Input Image
   <2>@{***X11}  ; Output stack
   B            ; Below
   X88          ; Threshold
   X41          ; Min

   VM
   echo "Slice: {***x11} TH F at Threshold "
   x11=x11+1   ; Increment stack pointer

EN