([prj-radius],[grp],[iter])
; Merge Volumes at end of defocus group loop
; SOURCE: endmerge.pam ArDean Leith Nov 2000
; [] ArDean Leith Dec 2005
; maxim ArDean Leith Dec 2006
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs
;
; INPUT REGISTERS:
; [prj-radius] Radius of restored object
; [grp] Group number
; [next-iter] Iteration number
;
; '##' denotes iteration, '##+' denotes next iteration, and '***' denotes group
; INPUT FILES:
; [order_select] input/order_select Group selection doc file
; [sel_particles] work/defgrp***/select Particle selection doc file
; [sel_particles_even] work/defgrp***/selecteven Particle selection doc file
; [sel_particles_odd] work/defgrp***/selectodd Particle selection doc file
; [next_group_align] final/defgrp***/align##+ Alignment parameter doc file
; [next_aligned_images] work/dala##_***@ Aligned images
;
; OUTPUT FILES:
; [next_group_bpr] final/defgrp***/bpr##+ Final reconstructed volume
; [next_group_bpr]_odd final/defgrp***/bpr_##+_odd Final odd reconstructed volume
; [next_group_bpr]_even final/defgrp***/bpr_##+_even Final even reconstructed volume
; [next_group_dbpr] final/defgrp***/dbpr##+ Resolution doc file
;
; CALLS: none
;......................................................................
[next-iter]=[iter]+1
VM
echo " endmerge starting for Group: {***[grp]}"
VM
date '+ TIME: %x %X'
FI X [maxim] ; Find total number of images (not same as in group selection)
[next_aligned_images] ; Aligned images (input)
(26) ; Header location for number of images in file
DE
_8@ ; If not deleted may overflow existing stack
; ; Calculate volumes using 'BP CG' for increased resolution
CP ; Load aligned projections into inline stack #8
[next_aligned_images] ; Aligned images (input)
_8@ ; Inline stack (output)
[maxim] ; Number of images (Not all in use)
BP CG ; Back Projection using conjugate gradients
_8@****** ; Template for image files (input)
[sel_particles] ; Particle selection doc. file (input)
[prj-radius] ; Radius of restored object
[next_group_align] ; Alignment parameters doc file (input)
N ; Does volume have symmetries
[next_group_bpr] ; Reconstructed volume file (output)
(1.0E-5,0.0) ; Error limit, chi^2 limit:
(25,1) ; Iteration limit, mode
(2000) ; Lambda
MY FL
; ; Two additional 'BP' runs to assess resolution
BP CG ; Back Projection - 3D, conjugate gradients
_8@****** ; Template for image files (input)
[sel_particles_odd] ; Odd particle selection doc. file (input)
[prj-radius] ; Radius of restored object
[next_group_align] ; Alignment parameters doc file (input)
N ; Does volume have symmetries
[next_group_bpr]_odd ; Reconstructed odd volume (output)
(1.0E-5,0.0) ; Error limit, chi^2 limit
(25,1) ; Iteration limit, mode
(2000) ; Lambda
MY FL
BP CG ; Back Projection - 3D, conjugate gradients
_8@****** ; Template for 2D image file (input)
[sel_particles_even] ; Even particle selection doc. file (input)
[prj-radius] ; Radius of restored object
[next_group_align] ; Alignment parameters doc file (input)
N ; Does volume have symmetries
[next_group_bpr]_even ; Reconstructed even volume (output)
(1.0E-5,0.0) ; Error limit, chi^2 limit
(25,1) ; Iteration limit, mode
(2000) ; Lambda
RF 3 ; Phase Residual & Fourier shell correlation
[next_group_bpr]_odd ; Odd volume (input)
[next_group_bpr]_even ; Even volume (input)
(0.5) ; Ring width
(0.2,2.0) ; Scale factor
C ; Missing cone or wedge
(90.0) ; Max. tilt angle
(3) ; Factor for noise comparison
[next_group_dbpr] ; Resolution doc file - dbpr (output)
MY FL
RE
;