([freq],[iter],[ampenhance])
;
; Merges groups at end of each refinement iteration
;
; SOURCE: spider/docs/techs/recon/newprogs/mergegroups.pam
; New ArDean Leith Nov 2000
; saveresp ArDean Leith Jan 2005
; Enhance ArDean Leith Apr 2005
; [] ArDean Leith Dec 2005
; Filenames ArDean Leith Dec 2009
; Echo format ArDean Leith Aug 2010
; CofG centering now done here ArDean Leith Sep 2010
; Ampl. enhancement moved out ArDean Leith Oct 2010
;
; PURPOSE: Consolidates goup volumes with CTF correction at end of each
; iteration into overeall volumes. Filters to limit resolution.
; (This is not done in parallel).
;
; CALLED FROM: pub_refine pub_refine.pam
;
; INPUT REGISTERS:
; [freq] Nyquist frequency for filtering
; [iter] Refinement step iteration counter
; [ampenhance] Flag to use amplitude enhancement
;
; '##' denotes iteration, '##+' denotes next iteration, '***' denotes group
; INPUT FILES:
; [sel_group_sorted] input/sel_group_sorted Sorted list of groups
; [temp_ctf_file_template] work/ctf*** 3D CTF files
; [next_group_vol_template] work/defgrp***/vol_## Group volume
; [next_group_vol_template]_sub1 work/defgrp***/vol_##_sub1 Group volume, deleted at end
; [next_group_vol_template]_sub2 work/defgrp***/vol_##_sub2 Group volume, deleted at end
; [mask] input/mask (Optional) Mask from original input volume
; OUTPUT FILES:
; [next_val] final/val## Unfiltered volume
; [next_vol]_filtered final/vol##_filtered Filtered volume
; [next_vol]_sub1 final/vol##_sub1 Filtered volume - subset 1
; [next_vol]_sub2 final/vol##_sub2 Filtered volume - subset 2
; [next_vol] final/vol## Shifted, filtered volume
; [next_dres] final/dres## Resolution doc.
; [enhance_doc] work/enhance_doc_##+ (Optional) Ampl filter doc. file
; [next_val]_amps final/val##+_amps (Optional) Ampl enhanced vol., unfiltered
;
;.......................................................................
; All defocus groups must be present here for "TF CTS" use!
[next-iter]=[iter] + 1 ; Next iteration
TF CTS ; Transfer Function - CTF Correction
[next_group_vol_template] ; Overall group volumes (input)
[sel_group_sorted] ; Group selection file (input)
[temp_ctf_file_template] ; 3D CTF files (input)
(3) ; SNR
[next_val] ; Overall CTF'd volume (output)
TF CTS ; Transfer Function - CTF Correction
[next_group_vol_template]_sub1 ; Subset 1 group volumes (input)
[sel_group_sorted] ; Group selection file (input)
[temp_ctf_file_template] ; 3D CTF files (input)
(3) ; SNR
[next_vol]_sub1 ; CTF'd volume - subset 1 (output)
TF CTS ; Transfer Function - CTF Correction
[next_group_vol_template]_sub2 ; Subset 2 group volumes (input)
[sel_group_sorted] ; Group Selection File (input)
[temp_ctf_file_template] ; 3D CTF files (input)
(3) ; SNR
[next_vol]_sub2 ; CTF'd volume - subset 2 (output)
DE
[next_dres] ; FSC doc file (removed)
; Resolution calculation
RF 3 [p69],[spfreq] ; Phase Residual & FSC
[next_vol]_sub1 ; Volume - subset 1 (input)
[next_vol]_sub2 ; Volume - subset 2 (input)
(0.5) ; Ring width
(0.2,2.0) ; Scale factor
C ; Missing cone/wedge angle
(90.0) ; Maximum tilt angle
(3) ; Factor for noise comparison
[next_dres] ; FSC doc file (output)
[grp] = 0 ; Defocus group is zero now (none)
@saveresp([freq],[iter],[grp],[spfreq]) ; Record resolution in doc file
[dbpr_resol] ; Resolution doc file (output)
IF ([ampenhance] .EQ. 0) THEN ; No amplitude enhancement (Usual case)
; Filter to limit resolution
IF([spfreq] .GT. 0.35)[spfreq] = 0.4 ; Limits pass-band
[stop-band] = [spfreq]+0.15 ; Stop band frequency
; Filter output volume to limit resolution
FQ ; Quick filter
[next_val] ; CTF'd volume (input)
[next_vol]_filtered ; Filtered volume (output)
(7) ; Butterworth Low pass filter
[spfreq],[stop-band] ; Pass-band and stop-band freq.
ELSE ; Use amplitude enhancement
; Apply amplitude enhancement filter and filter to limit resolution
@enhance([p69],[freq],[next-iter],[spfreq])
[next_val] ; Reconstructed volume (input)
[next_vol]_filtered ; Filtered volume (output)
ENDIF
; Find center of gravity of overall filtered volume
CG PH [unused],[unused],[unused],[xcg],[ycg],[zcg]
[next_vol]_filtered ; Filtered volume (input)
; Shift filtered vol to its CofG
SH F ; Shift filtered vol
[next_vol]_filtered ; Filtered volume (input)
[next_vol] ; Shifted filtered volume (output)
-[xcg],-[ycg],-[zcg] ; Shift distances for CofG
VM ; Delete files to save space
\rm [next_group_vol_template]_sub1* [next_group_vol_template]_sub2*
VM
echo -n " Iter: {**[iter]}" Shift: -{%F4.1%[xcg]},-{%F4.1%[ycg]},-{%F4.1%[zcg]} ; date '+ Time: %x %X'
MY FL
RE
;