; Apply rotational alignment to the particles that were already centered

; Number of particles
X91=3744

; Max radius for rotational alignment
x21=25

ap ra
center/PRK****
1-X91
5,x21
0
F
aprc/haldoc

; Rotate all the particles according to the angles from the
; document file produced by AP RA

do lb1 i=1,X91
x90=x0
ud ic,x90,x41,x42,x43,x44
aprc/haldoc
rt sq
center/PRK{****x41}
aprc/PRK{****x41}
x42
(0,0)
lb1
;

;  Prepare mask for PCA
; Get image dimensions
FI X41,X42
aprc/PRK0001
12,2

; Set mask radius to NSAM/2-1
X43=X41/2-1
mo
_1
X41,X42
C
X43

; Prepare SEQuential file
; Code number
X95=5

CA SI
aprc/PRK****
1-X91
_1
SEQ{***X95}
Y
0.0

; Perform PCA, get 20 factors
CA S
SEQ{***X95}
20,X95
Y
0

; Do the Hierarchical Clustering
CL HC
2
X95
1-20
0
2
N
Y
den001

; Calculate number of classes for a given threshold

CL HD
0.7
den001
how_many

; Create selection docfiles for a given threshold

CL HE
0.7
den001
grp/sel***

; Calculate group averages

UD N,X81
how_many
DO LB81 I=1,X81
X31=x0
AS DC
aprc/PRK****
grp/sel{***X31}
A
grp/avg{***X31}
grp/var{***X31}
LB81

; Calculate the resolution for each group

DO LB82 I=1,X81
X31=x0
AS DC
aprc/PRK****
grp/sel{***X31}
O
_1
_2
_3
_4
RF
_1
_3
(0.5)
(0.2,2.0)
grp/dres{***X31}
LB82

EN