; a batch program that does SACF 2D alignment.
; Pawel Penczek  Oct 2000
;

md
set mem
800
md
vb off
;
; number of images
UD N,X19
select194

x20=100  ; image size
x21=40   ; radius for alignment
x25=8    ; number of iterations of the multireference alignment

MO       ; MASK for RF SN
_9
x20,x20
C
x21

; create subdirectory for classification results &  averages
X81=1
VM
echo "if(-d stepi{***x81}) rm -r stepi{***x81}"|csh
VM
mkdir stepi{***x81}

; copy all the images
DO LB19 x92=1,x19
   CP
   files/spi{***x92}
   acng/data002@{***x92}
LB19
;
AS R
acng/data002@****
1-x19
A
stepi{***x81}/AVG001
stepi{***x81}/VAR001
CP
acng/data002@130
stepi{***x81}/AVG001
;
;  Calculate ACs
MS
_7@
175,175
x19
;  _6 - original images
MS
_6@
x20,x20
x19
DO LB71 x92=1,x19

MA
files/spi{***x92}
_6@{***x92}
(45)
G
C
(51,51)
(3.5)
PD
_6@{***x92}
_1
(175,175)
N
(0.0)
(38,38)
AC NS
_1
_7@{***x92}
LB71
;
; Iterate alignment
DO LB8 x81=1,x25
x82=x81+1
;
; Calculate AC of the current average
FD
stepi{***x81}/AVG001
_1
tanh
MA
_1
_3
(45)
G
C
(51,51)
(3.5)
PD
_3
_4
(175,175)
B
(38,38)
AC NS
_4
_1
FT
_3
_4
VM
echo "if(-d stepi{***x82}) rm -r stepi{***x82}"|csh
VM
mkdir stepi{***x82}
; Find all the angles
DO LB73 x92=1,x19
OR 2,X51
_7@{***x92}
_1
(5,75)
(1)
H
; Calculate CC with using the angle and angle+180
RT SQ
_6@{***x92}
_2
X51
(0,0)
CC
_2
_4
_3
PK X11,X12,X13,X14,X15,X16,X17
_3
(1,0)
X52=X51+180
RT SQ
_6@{***x92}
_8
X52
(0,0)
CC
_8
_4
_3
PK X11,X12,X13,X14,X65,X66,X67
_3
(1,0)
IF(X17.GT.X67)  THEN
RT SQ
_6@{***x92}
acng/data002@{***x92}
 X51
-X15,-X16
ELSE
RT SQ
_6@{***x92}
acng/data002@{***x92}
X52
-X65,-X66
ENDIF
LB73
;
;
AS R
acng/data002@****
1-x19
A
stepi{***x82}/AVG001
stepi{***x82}/VAR001
RT SQ
stepi{***x82}/AVG001
_1
(180)
(0,0
CC N
stepi{***x82}/AVG001
_1
_3
PK X11,X12,X13,X14,X15,X16,X17
_3
(1,0)
x15=-x15/2
x16=-x16/2
SH
stepi{***x82}/AVG001
_1
X15,X16
CP
_1
stepi{***x82}/AVG001
RF SN
acng/data002@****
1-x19
_9
(0.5)
stepi{***x82}/rfsn001

LB8

RE