([prj-radius],[grp],[iter])
; Merge volumes at end of defocus group loop
; SOURCE: spider/docs/techs/recon/newprogs/endmerge.pam
; new Nov 2000 ArDean Leith
; [] Dec 2005 ArDean Leith
; maxim Dec 2006 ArDean Leith
; group sel. filename Dec 2009 ArDean Leith
; echo format Aug 2010 ArDean Leith
; 'BP CG 3' Jan 2011 ArDean Leith
;
; INPUT REGISTERS: (Read from caller)
; [prj-radius] Radius of restored object
; [grp] Group number
; [next-iter] Iteration number
;
; '##' denotes iteration, '##+' denotes next iteration, '***' denotes group
; INPUT FILES:
; [sel_particles] input/select_*** Group particle selection doc file
; [next_group_align] final/align##+*** Alignment parameter doc file
;
; OUTPUT FILES:
; [next_group_bpr] final/bpr##+_*** Reconstructed group volume
; [next_group_bpr]_sub1 final/bpr##+_***_sub1 Group volume-sub1
; [next_group_bpr]_sub2 final/bpr##+_***_sub2 Group volume-sub2
; [next_group_dbpr] final/dbpr##+ Overall resolution doc file
;
; Uses inline stack file: _8
;......................................................................
[next-iter]=[iter]+1
VM
echo -n " Starting endmerge, Group: {***[grp]} --- " ; date '+ %x %X'
DE
_8@ ; If not deleted may overflow existing stack
FI H [maxim] ; Find total number of images (not same as in group selection)
[unaligned_images]@ ; Aligned images (input)
MAXIM ; Number of images in file
; Rarely the aligned projections may not fit in _8@, if not, use disk stack.
CP ; Load unaligned images into inline stack #8
[unaligned_images]@ ; Aligned images (input)
_8@ ; Inline stack (output)
[maxim] ; Number of images (Not all in use)
; Apply new transforms to original particle images
RT SQ ; Rotate & shift operation
_8@****** ; Unaligned original stacked images
[sel_particles] ; Particle selection file (input)
6,0,7,8 ; Reg. #s for angle, scale, & shift
[next_group_align] ; Alignment parameter doc file (input)
_8@****** ; Current aligned images (output)
; Calculate volumes using 'BP CG 3' (Gives better resolution than 'BP 32F').
BP CG 3 ; Back Projection - CG
_8@****** ; Template for image files (input)
[sel_particles] ; Group particle selection doc. file (input)
[prj-radius] ; Radius of restored object
[next_group_align] ; Alignment parameters doc file (input)
L ; Linear interpolation
[next_group_bpr] ; Reconstructed group volume (output)
[next_group_bpr]_sub1 ; Reconstructed group volume 1 (output)
[next_group_bpr]_sub2 ; Reconstructed group volume 2 (output)
1.0E-5,0.0 ; Error limit, chi^2 limit
25, 1 ; Iteration limit, mode
2000 ; Lambda
MY FL
; Assess group reconstruction resolution
RF 3 ; Phase Residual & FSC
[next_group_bpr]_sub1 ; Group subset volume 1 (input)
[next_group_bpr]_sub2 ; Group subset volume 2 (input)
0.5 ; Ring width
0.2, 2.0 ; Scale factor
C ; Missing cone or wedge
90.0 ; Max. tilt angle
3.0 ; Factor for noise comparison
[next_group_dbpr] ; Group resolution doc file (output)
DE
_8@
MY FL
RE
;