; Refined reference-based alignment
;
; PURPOSE: Refined reference-based alignment
; SOURCE: spider/docs/techs/align2d/refi-ref-ali.spi
;
; I/O PARAMETERS AND FILES ARE SET HERE:
[npart] = 20 ; Number of particles
[nref] = 1 ; Number of reference images
[r1] = 4 ; First ring for rotational alignment
[r2] = 25 ; Last ring for rotational alignment
[shrange] = 4 ; Search range (translations restricted to +/- this range)
[skip] = 1 ; Search range skip.
[niter] = 7 ; Number of iterations
; ------------ Input files ---------------------------------------
[unaligned] = 'input/savface_stk_rotsh@' ; Unaligned particle image stack
; --------------- Output files -----------------------------------
[select] = 'output/refi_select_doc' ; Selected particle numbers
[aligned] = 'output/refi_ali_' ; Aligned particle image stacks
[ref] = 'output/refi_ref@' ; Reference image stack
[frcdoc] = 'output/refi_dres_doc_' ; FRC curve doc file stem
[align] = 'output/refi_ali_doc_' ; Alignment doc file stem
[avgodd] = '_1' ; Avg odd
[avgeven] = '_2' ; Avg even
; -------------- END BATCH HEADER ---------------------------------
MD
VB OFF
; Create a selection document file. (This image series is consecutive)
DOC CREATE
[select] ; Selection doc file (output)
1 ; Register
1-[npart] ; Particle numbers
CP ; Copy input files to output stack
[unaligned] ; Unaligned article images (input)
[aligned]001@ ; Aligned particle images (output)
DO [iter]=1,[niter] ; Iteration loop ---------------------
; Create a reference by averaging all images
AS S ; Sum all images
[aligned]{***[iter]}@**** ; Aligned images (input)
[select] ; Particle select file (input)
AS ; All images
[ref]{***[iter]} ; Ref image in stack (output)
[avgodd] ; Avg of odd (output)
[avgeven] ; Avg of even (output)
; Determine resolution
DE
[frcdoc]{***[iter]} ; FRC doc file (removed)
FRC [half],[res] ; Fourier ring correlation
[avgodd] ; Avg of odd (input)
[avgeven] ; Avg of even (input)
0.5 ; Ring width
1 ; Arbitrary pixel size
[frcdoc]{***[iter]} ; FRC doc file (output)
* ; No FRC plot file
VM
echo ' Iteration: {**[iter]} Relative Res:{%f6.1%[res]}'
IF([iter] >= [niter]) EXIT ; Finished
; Alignment
[itert] = [iter] + 1
DE
[align]{***[itert]} ; Align. doc file (removed)
AP SH
[ref]*** ; Ref image stack (input)
[iter] ; Ref number in stack
[shrange],[skip] ; Shift
[r1],[r2] ; Polar rings
* ; No ref images angles file
[aligned]{***[iter]}@**** ; Exp. images (input)
[select] ; Selection file (input)
* ; Exp images alignment doc file
0,0 ; Range of proj angle search
Y ; Check mirrored postions, rtsq
[align]{***[itert]} ; Align. doc file (output)
; Rotate/shift images according to alignment parameters
RT SF ; Since consecutive can use whole stack operation
[aligned]{***[iter]}@**** ; Aligned image stack (input)
[select] ; Particle selection file (input)
12,0,13,14 ; Rot, scale, & shift registers
[align]{***[itert]} ; Alignment doc file (input)
[aligned]{***[itert]}@**** ; Aligned image stack (output)
ENDDO
EN