; rctcenl: 
;
;        reads all angles from the label of the tilt images
;        (currently 2 questions just dummied out)
;procedure to center the tilted images directly by cross-correlation
;with the untilted ones
;three rounds of cross-correlation are done
;;author:m.radermacher
;converted to new spider d.bubeck 7/2/97 
;--------------------------------------------------------------------
;
;create blank file:
bl
scr997
32,32
n
0
; get input data:
fi
?windowed original tilted input image names?
;----------------------------------------------------p1
fi
?aligned untilted input image name (must exist)?
;----------------------------------------------------p2
x30=x1
x31=x2
rr x10
?first key in selection doc-file?
;----------------------------------------------------p3
rr x11
?last key in selection doc-file?
;----------------------------------------------------p4
fi
?lookup output files?
;----------------------------------------------------p5
rr x50
?mask radius?
;----------------------------------------------------p6
fr
?tilted centered output files?
;----------------------------------------------------p7
x32=x30/2+1
x33=x31/2+1
;----------------------------------------------------
; cross correlate tilted images with untilted to center them
;--------------------------------------------------
fr
?selection doc-file?
;----------------------------------------------------<8>
fr
?output shift docfile?
;----------------------------------------------------<9>
fr
?output lookup montage?
;----------------------------------------------------<10>    10
rr x25
?low pass radius?
;----------------------------------------------------<11>
rr x26
?high pass radius?
;----------------------------------------------------<12>
do lb3 i=x10,x11
x94=x0
ud x0,x86
<8>
if(x86.ne.1.)goto lb3
fi x20,x21
<1>x94
15,16
;--------------------tilt angle parameters, x20 phi,x21 theta
if(x21.eq.0) goto lb5
x62=x21
x63=cos(x62)
x64=x30/x63
x65=((x64-x31)/2+1)
x66=1
x87=2.6
;------------------------------------------------tilted
;------strech the tilted one
ip
<1>x94
scr000
x64,x30
wi
scr000
scr001
x30,x31
x65,x66
;----------------mask the tilted streched
ma
scr001
mmf001
x50
g
a
x32,x33
x87
;---------------------------------------------------untilted
;-----rotate, mask, low-pass and high-pass the untilted
;
rt
<2>x94
scr001
x20
;
ma
scr001
scr999
x50
g
a
x32,x33
x87
;
ft ic
scr999
_1
ff
_1
_2
(3)
x25
ff
_2
_3
(4)
x26
ft 
_3
scr999
;------------------------------------------------cross-correlation
;------------first time
cc 
mmf001
scr999
ccf001
x51=(x30/2-x50)+2 
;(distance for edge exclusion)
;             
;                          find peak of the cross-correlation
;wi
;ccf001
;cct1lx94
;(32,32)
;(49,49)
pk c x40,x41           
ccf001
(3,0)
(12.,12.)
y
(2.)
x51
x40=x40*x63
;
sh f
<1>x94
scr002
-x40,-x41
;
;  second time
;------------------------------------------redo the work with the shifted unt.
;------strech the new tilted one
ip
scr002
scr000
x64,x30
wi
scr000
scr001
x30,x31
x65,x66
;----------------mask the new tilted streched
ma
scr001
mmf001
x50
g
a
x32,x33
x87
;--------------cross-correlation
cc 
mmf001
scr999
ccf001
x51=(x30/2-x50)+2 
;(distance for edge exclusion)
;             
;                          find peak of the cross-correlation
;wi
;ccf001
;cct2lx94
;(32,32)
;(49,49)
pk c x90,x91           
ccf001
(3,0)
(12.,12.)
y
(2.)
x51
x90=x90*x63
;                          shift the original image by the combined vector
;
x84=x90+x40
x85=x91+x41
sh f
<1>x94
scr002
-x84,-x85
;
;
;  third time
;------------------------------------------redo the work with the shifted unt.
;------strech the new tilted one
ip
scr002
scr000
x64,x30
wi
scr000
scr001
x30,x31
x65,x66
;----------------mask the new tilted streched
ma
scr001
mmf001
x50
g
a
x32,x33
x87
;--------------cross-correlation
cc 
mmf001
scr999
ccf001
x51=(x30/2-x50)+2 
;(distance for edge exclusion)
;             
;                          find peak of the cross-correlation
;wi
;ccf001
;cct3lx94
;(32,32)
;(49,49)
pk c x80,x81           
ccf001
(3,0)
(12.,12.)
y
(2.)
x51
x80=x80*x63
;                          shift the original image by the combined vector
;
x84=x90+x40+x80
x85=x91+x41+x81
sh f
<1>x94
<7>x94
-x84,-x85
;
;
;                          save the shift parameter
;
sd x0,x40,x41,x90,x91,x80,x81
<9>
sd x0,x84,x85
<9>
;                          interpolate down
x47=x30/x32+1
bc
<7>x94
scr995
l
(5,5)
(1)
ip
scr995
scr998
(32)
;                          find dynamic range for display
fs
scr998
fi
scr998
x71=x5+3*x6
x70=x5-3*x6
th
scr998
<5>x94
c
x71,x70
;
lb3
mn s
<5>
x10-x11
(10,1)
(0)
<10> 
if(x21.ne.0) goto lb6
lb5
;******* image header empty **********
lb6
re