; RUN REFERENCE-FREE ALIGNMENT
;
; Using SPIDER command AP SR

; ---------------- Parameters ----------------
x55 = 5        ; first ring radius for alignment, pixels
x60 = 88       ; expected object diameter, pixels

; ---------------- Input files ----------------
fr g
[group_particles]listparticles  ; group-particle list
fr g
[unaligned]flt/flt******        ; filtered particles

; --------------- Output files ---------------
fr g
[apsr_dir]apsr                    ; output AP SR directory
fr g
[apsr_avg][apsr_dir]/iteravg***   ; reference-free average template
fr g
[apsr_doc][apsr_dir]/docapsr***   ; reference-free alignment doc template
fr g
[aligned_dir]ali                  ; output aligned directory
fr g
[aligned][aligned_dir]/sar******  ; aligned particles

; ------------- END BATCH HEADER -------------

vm
echo "Performing reference-free alignment"; date

vm
echo "if(! -d [apsr_dir]) mkdir -p [apsr_dir]"|csh
vm
echo "if(! -d [aligned_dir]) mkdir -p [aligned_dir]"|csh

; GET IMAGE DIMENSION

; get 1st particle#
ud 1,x13
[group_particles]
ud e  ; close doc

; get image dimension
fi x65
[unaligned]x13
(12)  ; header position for x-dim

; calculate center coordinate
x32 = (x65+1)/2

; calculate radius for last alignment ring
x30=(x60-1)/2


; GENERATE BLOB FOR CENTRATION

; generate disc
pt
_1       ; OUTPUT
x65,x65  ; dimensions
C        ; _C_ircle
x32,x32  ; center coords
x30      ; object radius
N        ; continue?

; low-pass filter disc
fq
_1      ; INPUT
_2      ; OUTPUT
(3)     ; Gaussian low-pass
(0.02)  ; filter radius

;; use all processors
;md
;set mp
;(0)

; run reference-free alignment
AP SR
[unaligned]        ; particles to be aligned
[group_particles]  ; selection file
x60                ; expected size of the object
x55,x30            ; first and last ring radius
_2                 ; centering image
[apsr_avg]
[apsr_doc]
 

; COUNT #ITERATIONS

x31=100  ; max #iterations

; loop through iterations
do lb1 x20=1,x31
    ; check if file exists
    iq fi x33
    [apsr_doc]x20
 
    ; if file doesn't exist, then exit loop
    if (x33.lt.1) goto lb7
lb1
; end iteration-loop
 
lb7  ; jump here when iteration file not found

x88=x20-1  ; previous iteration's file exists


vm
echo "Aligning particles"; date

; get #particles
ud n x11
[group_particles]

; loop through particles
DO LB2 x12=1,x11
    ; get particle#
    ud ic,x12,x13
    [group_particles]

    ; get alignment parameters
    UD IC, x12,x21,x22,x23
    [apsr_doc]x88
 
    RT SQ
    [unaligned]x13
    [aligned]x13
    (x21,1)  ; angle, scale
    x22,x23  ; x,y-shift
LB2
; end particle-loop
 
ud ice
[group_particles]
UD ICE
[apsr_doc]x88
 
vm
echo "Done"; date

en d

; Modified 2009-06-12
;    2008-11-12 (trs & th) -- generates centration reference
;    2008-04-10 (trs) -- seems to dump core if all processors used
;    2008-04-02 (trs & th) -- bug fix for AP SR iteration-counter
;    2007-11-20 (trs & djt) -- bug fix for non-consecutive selection file
;    2007-11-01 (trs) -- adapted from common-lines tutorial