([ang-step],[ang-limit],[radius],[alignsh],[prj-radius],[iter],[grp],[toobig],[maxspfreq])
; Main refinement group loop
;
; SOURCE: grploop.pam Original ArDean Leith Nov 2000
; %degredations ArDean Leith Feb 2005
; [] ArDean Leith Dec 2005
; More stacks & 'RT SQ' selection ArDean Leith Dec 2006
; 'AP SH' use ArDean Leith Feb 2007
; tmp dir purge ArDean Leith Mar 2008
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; PURPOSE: Main refinement group loop. Runs for each defocus group on each iteration
;
; CALLED FROM: pub_refine_start or
; refine.pam
;
; INPUT REGISTERS:
; [ang-step] Angular steps (varies with iter)
; [ang-limit] Restrict angular search (varies with iter)
; [radius] Radius of the structure (pixels)
; [alignsh] Shift allowed is +-[alignsh]
; [prj-radius] Radius of the structure used in projection
; [iter] Alignment step iteration counter (varies with iter)
; [grp] Defocus group (varies with group)
;
; OUTPUT REGISTERS:
; [toobig] % of images whose proj. angle moved by > 1.5*[ang-step]
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES (SET IN: refine_settings refine_settings.pam.pam):
; [order_select] input/order_select Image ID doc. fil
; [sorted_order_select] input/order_select_sort Image ID doc. fil
; [sel_particles] input/select_*** Particle selection file
; [iter_vft] final/vft## Current filtered volume
; [temp_ctf_file] work/ctf*** CTF corrected volume from prepare
; [aligned_images] input/dala##_*** Aligned stacked image files
; [group_align] final/align##+_*** Alignment parameter doc file
; [unaligned_images] input/data*** Unaligned stacked image files
; [iter_ang_voea] final/angvoea_## Ref. angles doc. file
; [iter_select_voea] final/selvoea_## Ref. angles selection doc. file
;
; OUTPUT FILES (SET IN: refine_settings refine_settings.pam.pam):
; [next_group_align] final/align##_*** Alignment parameter doc file
; [next_aligned_images] work/dala##+_***@ Aligned stacked image files
; [next_group_vol] work/defgrp***/vol## Reconstructed volume
; [next_group_dres] final/defgrp***/dres##+ Resolution curve doc. file
; [next_group_vol]_odd work/defgrp***/vol_##+_odd (created & deleted)
; [next_group_vol]_even work/defgrp***/vol_##+_even (created & deleted)
; [temp_ref_projs] /tmp/refproj##_*** (created & deleted)
;
; PROCEDURES CALLED: saveresp
;
; INLINE BUFFERS USED: _1, _4, _8
VM
echo " In grploop, Iteration: {**[iter]} Group: {***[grp]}"
VM
date '+ Time: %x %X'
[radius1]=5.0 ; First radius for AP (Can alter this)
[ang-change-thresh]=1.5*[ang-step] ; Convergence criterion ang. distance limit.
[next-iter]=[iter]+1
UD N [num-refs] ; Get number of reference images used
[iter_select_voea] ; Ref. angles selection doc. file (input)
UD N,[numgrps] ; Find number of defocus groups
[sorted_order_select] ; (input)
; Get number of images in this group
DO LB1 [i]=1,[numgrps] ; Loop over defocus groups -----------
; GROUP, PART.
UD IC [i], [grpt], [numparts] ; Get number of particles
[sorted_order_select] ; Doc file listing groups (input)
IF ([grpt].EQ.[grp])GOTO LB2
LB1
LB2 ; Got number of particles in this group
UD ICE
[sorted_order_select]
; Multiply Fourier of current volume by CTF file for this group
MU ; Multiply
[iter_vft] ; Fourier of current volume (input}
[temp_ctf_file] ; CTF file (work/ctf{grp}) (input)
_1 ; _1 created here (output)
* ; End multiplications
FT ; Fourier back transform
_1 ; Fourier of CTF corrected volume (input)
_4 ; CTF corrected current volume (output)
DE ; _1 can be deleted here
_1 ; Fourier of CTF corrected current volume
MY FL ; Flush results file
; Clear tmp directory and create temp local dir., divert errors to junk
VM
\rm -rf /tmp/* >& /dev/null
VM
mkdir -p [temp_local_dir]
VM ; So anyone can delete it
chmod 777 [temp_local_dir]
; Create stack holding angular reference projections from CTF corrected volume.
PJ 3Q ; Create reference projections
_4 ; CTF corrected current volume (input)
[prj-radius] ; Radius of object
[iter_select_voea] ; Ref. angles selection doc. file (input)
[iter_ang_voea] ; Ref. angles doc. file (input)
[temp_ref_projs]@****** ; Template for ref. projections (output)
DE ; _4 can be deleted here
_4 ; CTF corrected current volume
FI X [maxim] ; Find total number of images (not [numparts])
[aligned_images] ; Input file needed (input)
(26) ; Max. image number header position
CP ; Copy current aligned images to inline stack
[aligned_images] ; Input file needed (input)
_8@ ; Current aligned images stack (output)
[maxim] ; Number of images in stack _8@
DE ; Remove existing alignment doc file
[next_group_align] ; Alignment parameter doc file
DE ; Remove existing scratch file
work/SCR_{**[iter]}_{***[grp]} ; Reference rings scratch file
MY FL ; Flush results file
[useapsh]= 0 ; Do not use 'AP SH' (Can change this)
IF ([iter] .GT. 1) THEN
[useapsh] = 0 ; Use 'AP REF'instead of 'AP SH'
ENDIF
; Find reference projection matching current aligned image
; (For large images change 'skip' to 2 or 3 to decrease memory)
IF ([useapsh] .EQ. 1) THEN
; 'AP SH' gives more exhaustive search than 'AP REF' but is 4-5x slower
AP SH
[temp_ref_projs]@****** ; Template for ref. projections (input)
(1-[num-refs]) ; Ref. projections file numbers
([alignsh],1) ; Shift search range, Step size
([radius1],[radius],1) ; First, last radial ring, & skip
[iter_ang_voea] ; Ref. angles file (input)
_8@****** ; Template for exp. aligned images (input)
[sel_particles] ; Particle selection files (input)
[group_align] ; Alignment parameter doc. file (input)
[ang-limit],[ang-change-thresh] ; Angular search restriction
(1) ; Check mirrored projections
[next_group_align] ; Alignment parameter doc file (output)
; Default for unknown return value
[toobig]= 100
VM
echo " Iteration: {**[iter]} Group: {*****[grp]} "
ELSE
AP REF
[temp_ref_projs]@****** ; Template for ref. projections (input)
(1-[num-refs]) ; Ref. projections file numbers
[alignsh] ; Shift search range
([radius1],[radius],1) ; First, last radial ring, & skip
[iter_ang_voea] ; Ref. angles file (input)
work/SCR_{**[iter]}_{***[grp]} ; No scratch file if fits in-core
_8@****** ; Template for exp. aligned images (input)
[sel_particles] ; Particle selection files (input)
[group_align] ; Alignment parameter doc. file (input)
[ang-limit],[ang-change-thresh] ; Angular search restriction
(1) ; Check mirrored projections
[next_group_align] ; Alignment parameter doc file (output)
; Check size of change in proj. angle
; %BIG-ANGDIF, AVG-ANGDIF, AVG-CCROT, %WORSE, AVG-WORSE, AVG-BETTER
UD -2,[percent-greater],[AVG-ANGDIF],[avg-ccrot],[degred],[avg-degred],[avg-impr]
[next_group_align] ; Alignment parameter doc file (input)
UD E ; Close doc file access
; Return % of image whose proj. angle moved by > 1.5*[ang-step] criterion
[toobig]=[percent-greater]* 100
VM
echo " Iteration: {**[iter]} Group: {*****[grp]} Excessive changes: {%f8.2%[percent-greater]}% "
VM
echo " CCROT Degredation: {***[degred]}% Avg. degred.: {%F8.2%[avg-degred]} Avg. improve.: {%F8.2%[avg-impr]}"
ENDIF
; Apply transformations to all original particle images
RT SQ ; Rotate & shift operation
[unaligned_images]@****** ; Unaligned original stacked images
[sel_particles] ; Particle selection file (input)
(6,0,7,8) ; Reg. numbers for angle, scale, & shift
[next_group_align] ; Alignment parameter doc file (input)
_8@****** ; Current aligned images (output)
; Store aligned projections (Do now in case BP fails)
CP ; Create hard copy of aligned images
_8@ ; Aligned images in inline file (input)
[next_aligned_images] ; On disk file (output)
VM ; Echo for isolating stack overflow
echo " Back projecting group: {*****[grp]}"
MY FL
; Calculate new, refined volume using centered projections and
; the corrected angles from align doc. file. Creates two additional
; volumes from odd/even images for use in resolution calculation.
; (If you have large images which give problems allocating memory in 'BP 32F',
; substitute operation 'BP 3F'. Use that operation three times (with 3
; appropriate selection files for the images to be included) to create
; the three output volumes one by one.)
BP 32F ; Back Projection - 3D Fourier
_8@****** ; Template for current aligned images (input)
[sel_particles] ; Particle selection doc. file (input)
[next_group_align] ; Alignment parameter doc file (input)
* ; No symmetries
[next_group_vol]tmp ; Reconstructed 3D file (output)
[next_group_vol]_odd ; Reconstructed 3D file (output)
[next_group_vol]_even ; Reconstructed 3D file (output)
DE ; _8 no longer needed
_8
MY FL ; Flush results file
; Find center of gravity of the temp. volume
CG PH [unused],[unused],[unused],[xcg],[ycg],[zcg] ; Center of Gravity of vol.
[next_group_vol]tmp ; Volume (input)
SH F ; Shift temp volume to its center of gravity
[next_group_vol]tmp ; Temp. volume file (input)
[next_group_vol] ; Final group volume (output)
-[xcg],-[ycg],-[zcg] ; Shift
DE ; Delete temp volume file
[next_group_vol]tmp
RF 3 [unused],[spfreq] ; Find phase residual & shell correl.
[next_group_vol]_odd ; First volume file (input)
[next_group_vol]_even ; Second volume file (input)
(0.5) ; Ring width
(0.2,2.0) ; Lower and upper scale factor
C ; Missing cone
(90.0) ; Maximum tilt angle
(3) ; Factor for noise comparison
[next_group_dres] ; Resolution document file (output)
; Record this groups reconstruction resolution in doc file
@saveresp([maxspfreq],[iter],[grp],[spfreq])
[grp_resol] ; Resolution summary file (output)
VM ; Remove - refproj (no longer needed)
\rm -f [temp_ref_projs]*.$DATEXT
IF ([iter] .GT. 1) THEN ; Not first iteration
DE ; Remove previous group vol.
[group_vol] ; work/vol_{**[iter]}_{***[grp]}
DE ; Remove previous odd group vol.
[group_vol]_odd ; work/vol_{**[iter]}_{***[grp]}_odd
DE ; Remove previous even group vol.
[group_vol]_even ; work/vol_{**[iter]}_{***[grp]}_even
DE ; Remove previous current aligned images
[aligned_images_prefix] ; work/dala{**[iter]}_{***[grp]}
ENDIF
MY FL
RE
;