; Controls and synchronizes alignment
; apsh_pub.bat Mar 2003 ArDean Leith
; From apmq_pub Feb 2005 ArDean Leith
;
; Multireference alignment of an image series.
; Sample images are aligned with reference projections via shifts (translations)
; and rotations. For project with multiple micrographs. The work
; is partitioned into sets of images. The number of images in a set can be
; less than the number used in a whole micrograph.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs/
;
; INSTRUCTIONS: apsh_pub.html
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
;------------ Edit next 5 Alignment parameters ---------------------
; -------------- DO NOT COPY FROM WEB BROWSER ---------------------
x16 = 25 ; Number of images / partition set
x31 = 5 ; Translation search range (must be divisible by step size)
x32 = 1 ; Translation step size
x21 = 5 ; Rotation first ring, only radii within specified rings will be analyzed
x22 = 30 ; Rotation last ring, if pixel size is different than 4.78, change the rings
; ----------------- Input files, May have to edit these names ---------
FR G
[micrograph_selection_file]input/selmcg ; Micrograph selection doc. file
FR G
[ref_images_template]input/proj**** ; Reference image name template
FR G
[ref_images_selection]input/selref ; Reference images selection doc. file
FR G
[ref_images_angles]input/refangles ; Reference images angles doc. file
FR G
[sample_images_template]input/data{***x55}@**** ; Sample image name template
FR G
[sample_images_selection]input/selimg ; Sample images selection doc. file
; ----------------- Output file, May want to edit this name --------
FR G
[align_parameters]output/jnk_apsh ; Alignment parameters doc. file stem
;
; ----------------- Temporary Output file ----------------------------
FR G
[sync_doc]output/jnk_sync ; Sync doc. file stem
; --------------------------------------------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
IF (x14 .NE. 1) THEN ; Primary PubSub run creates parallel processes
; Get number of micrographs from micrograph selection file
; If you do not have a "micrograph selection file" you can
; create it using: 'DOC CREATE' and inputting the number of micrographs
UD N,x20
[micrograph_selection_file]
; Loop over all entries in micrograph selection file
x45=0 ; Set number
DO LB1 x11=1,x20
; Get micrograph file-number from micrograph selection file
UD x11,x55 ; Current micrograph number = x55
[micrograph_selection_file]
; Get image numbers in this micrograph from image selection file
UD x55,x43 ;
[sample_images_selection]
x40 = 1 ; Starting image
DO LB2 x42=1,1000000 ; Loop over all image sets
x41 = x40 + x16 - 1 ; Final image for this image set
IF (x41.GT.x43) x41=x43 ; Final image for this image set
x45 = x45 + 1 ; Set number
; Use PubSub to create parallel 'AP SH' process for each image set
VM
publish './spider bat/$DATEXT @apsh_pub {***x45} x14=1 x55={***x55} x45={****x45} x40={****x40} x41={****x41}'
IF (x41.GE.x43) GOTO LB99 ; Final image set for this micrograph
x40 = x41 + 1 ; Increment for next starting image
MY FL ; Flush results file
LB2
LB99
LB1
ELSE ; Secondary PubSub run (does actual alignments)
MD
SET MP ; Use all processors (needed here for secondary runs)
0
DE ; Delete existing alignment parameter output doc. files.
[align_parameters]_{***x55}_{****x45}
AP SH ; Align sample images using Multireference Method
[ref_images_template] ; Reference image name template (input)
[ref_images_selection] ; Reference images selection doc. file (input)
x31,x32 ; Search range, step size
x21,x22 ; First and last ring
[ref_images_angles] ; Reference images angles doc. file (input)
[sample_images_template] ; Sample images name template (input)
x40-x41 ; Sample image numbers
* ; No sample images alignment angles doc. file
(0) ; No resturiction on angles
(0) ; Check mirrored projections
[align_parameters]_{***x55}_{****x45} ; Alignment angles doc. file (output)
SD 1,x40,x41 ; Sync doc. file created when finished
[sync_doc]_{****x45}
SD E
[sync_doc]_{****x45}
EN
ENDIF
LB99
; Wait till all angular output files complete
x29=1
@wait_pub(x29,x45)
; Loop over all entries in micrograph selection file, combining the angular output files
DO LB3 x11=1,x20
DE
[align_parameters]_{***x11} ; Alignment angles doc. file (output)
VM
cat [align_parameters]_{***x11}_* > [align_parameters]_{***x11}_tmp.$DATEXT
DOC REN
[align_parameters]_{***x11}_tmp
[align_parameters]_{***x11}
VM
\rm -f [align_parameters]_{***x11}_* [sync_doc]*
LB3
EN ; This SPIDER ends now
;