[x77,x52,x58,x59,x51,x41,x42]
;Modified for 4-fold symmetry by M. Samso 8/27/99
; x77 - number of input images 
; x52 - image size
; x58 - image center
; x59 - allowed shift
; x51 - object radius
; x41 - theta step
; x42 -range of angular search
x78=1.0
; x54 - first radius for AP MD
x54=5.0
; x56 - double the size
x56=2*x52
;  Shift allowed is +-x59, input images are padded
x57=2*x59+1
x55=x52-x59+1
; center of the windowed CCF is at
x60=x59+1
;.....................................................................
;  inline buffer used: 1,2,3 and 9 as a stack
;.....................................................................
FR
?Reference volume?<1>
;   volx76
FR
?Input image series?<2>
;   original data _7
FR
?Output image series?<3>
;   prealigned data _8
FR
?apmd doc file from APRD?<4>
;   apmdx86
FR
?Input angular doc file?<10>
;   anglesx76
FR
?Output angular doc file?<5>
;   anglesx86
FR
?Transformation doc file from the previous step?<6>
;   transx76
FR
?New transformation doc file?<9>
;   transx86
FR
?Temporary angular doc file for APRD?<7>
;   angvoea
FR
?Temporary selection doc file for APRD?<8>
;   selvoea
;.....................................................................
MD
TR OFF
; x53 - number of reference projections
VO EA,x53
x41
(0,90.0)
(0,89.9)
<7>
DO LB26 i=x78,x53
SD x0,x0
<8>
LB26
SD E
<8>
;
MS
_9@
X52,X52,X78
X53
; Use AP RD command to match original projections to the reference
; projections.
PJ 3Q
<1>
x51
<8>
<7>
_9@*****
;
AP RD
_9@*****
x78-x53
x54,x51
(0)
<7>
N
<3>
X78-X77
<10>
x42
<4>
;
; use crosscorrelation to center 2D images
; use already calculated projections as reference images
; calculate shifts,  x53 used there !
;MD
;SET MP
;(4)
; x91 - average correlation coefficient
x91=0.0
;
DO LB5 i=x78,x77
x21=x0
UD S,x21,x81,x82,x83
<4>
; Rotate the image
RT SQ
<3>x21
_1
x83
(0,0)
;
; get corresponding reference projection,
; number is stored in apmd (x81)
x94=0
if(x81.gt.x53) then
; experimental image has to be mirrored
x94=1
x81=x81-x53
MR
_1
_2
Y
PD
_2
_3
x56,x56
N
(0.000E+00)
(1,1)
;
else
PD
_1
_3
x56,x56
B
(1,1)
endif
; get angles
ud ic,x81,x67,x68,x69
<7>
sd x21,x67,x68,x69
<5>
; padd reference image
pd
_9@00x81
_2
x56,x56
N
(0.000E+00)
(1,1)
; calculate cross-correlation
CC N
_3
_2
_3
;
WI
_3
_2
x57,x57
x55,x55
PK x10,x11,x12,x13,x31,x32,x33
_2
(0)
; when there was no peak found translation is (0,0) and peak value
; x33 is 0.  In this case get a value at the origin of the CCF
; and store in in shift document file.  This value is needed for
; sorting and calculation of the average correlation coeff.
IF(x33.eq.0.0)  then
GP x33
_2
x60,x60
ENDIF
; get the average correlation coefficient.
x91=x91+x33
;
x31=-x31
x32=-x32
; combine rotation, mirror, and shift and use RT SQ
if(x94.eq.1) then
x31=-x31
endif
; combine with the previous transformation
; Format of the transformation parameters doc file is:
;  angle, Sx, Sy, 0-1 flag for Y-mirror (0-no mirror; 1-mirror)
ud ic,x21,x23,x24,x25,x29
<6>
@combat[x23,x24,x25,x29,x83,x31,x32,x94,x61,x62,x63,x64]
sd x21,x61,x62,x63,x64
<9>
; apply combined transformation to the original experimental image
if(x64.eq.0) then
rt sq
<2>x21
<3>x21
x61
x62,x63
else
rt sq
<2>x21
_1
x61
x62,x63
mr
_1
<3>x21
Y
endif
LB5
;
x91=x91/x77
SD -1,x91
<9>
SD E
<9>
ud ice
<6>
sd e
<5>
; remove inline files
de
_1
de
_2
de
_3
de
_9@
; remove temporary files
ud ice
<7>
de
<7>
de
<8>
RE