([pixsiz],[iter],[ampenhance],[rm])
;
; Merges groups at end of each refinement iteration
;
; SOURCE: spider/docs/techs/recon/newprogs/mergegroups.pam
; New ArDean Leith Nov 2000
; Enhance ArDean Leith Apr 2005
; CofG centering now done here ArDean Leith Sep 2010
; Ampl. enhancement moved out ArDean Leith Oct 2010
; FSC, pixsiz ArDean Leith Aug 2012
; [xsh] ArDean Leith Apr 2015
;
; 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:
; [pixsiz] Pixel size
; [iter] Refinement step iteration counter
; [ampenhance] Flag to use amplitude enhancement
; [rm] Radius of object
;
; '##' denotes iteration, '##+' denotes next iteration, '***' denotes group
; INPUT FILES:
; [sel_group] input/sel_group List of groups
; [temp_ctf_file_template] work/ctf*** 3D CTF files
; [next_group_vol_template] work/vol_## Group volume
; [next_group_vol_template]_sub1 work/vol_##_sub1 Group volume, deleted at end
; [next_group_vol_template]_sub2 work/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]_sub1 final/vol##_sub1 Unfiltered volume - subset 1
; [next_vol]_sub2 final/vol##_sub2 Unfiltered volume - subset 2
; [next_vol]_filtered final/vol##_filtered Filtered volume
; [next_vol] final/vol## Shifted, filtered volume
; [next_fsc] final/fscdoc## 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 ; CTF Correction
[next_group_vol_template] ; Overall group volumes (input)
[sel_group] ; Group selection file (input)
[temp_ctf_file_template] ; 3D CTF files (input)
3 ; SNR
[next_val] ; Overall CTF'd volume (output)
TF CTS ; CTF Correction
[next_group_vol_template]_sub1 ; Subset 1 group volumes (input)
[sel_group] ; 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 ; CTF Correction
[next_group_vol_template]_sub2 ; Subset 2 group volumes (input)
[sel_group] ; Group Selection File (input)
[temp_ctf_file_template] ; 3D CTF files (input)
3 ; SNR
[next_vol]_sub2 ; CTF'd volume - subset 2 (output)
; Resolution calculation
DE
[next_fsc] ; FSC doc file (removed)
FSC [half],[spfreq],[res] ; Find phase residual & shell correl.
[next_vol]_sub1 ; Volume - subset 1 (input)
[next_vol]_sub2 ; Volume - subset 2 (input)
0.5,[rm] ; Shell width
[pixsiz] ; Pixel size
[next_fsc] ; FSC doc file (output)
* ; No Gnuplot file
SYS
echo " Iteration: {%I0%[iter]} Resolution: {%f6.2%[res]}"
[gr] = 0 ; Defocus group is zero now (none)
SD [iter], [iter],[gr],[res] ; Save in doc file
[iter_resol] ; Resolution doc file (output)
IF ( [ampenhance] == 0 ) THEN
; Usual case. No amplitude enhancement. Filter to limit resolution
IF( [spfreq] > 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 reconstructed volume (input)
[next_vol]_filtered ; Filtered volume (output)
7 ; Butterworth Low pass filter
[spfreq],[stop-band] ; Pass-band and stop-band freq.
ELSE
; Apply amplitude enhancement filter and filter to limit resolution
@enhance([p69],[pixsiz],[next-iter],[spfreq])
[next_val] ; CTF'd 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 Center of Gravity
SH F ; Shift filtered vol
[next_vol]_filtered ; Filtered volume (input)
[next_vol] ; Shifted filtered volume (output)
-[xcg],-[ycg],-[zcg] ; Shift distances for CofG
SYS ; Delete files to save space
\rm [next_group_vol_template]_sub1* [next_group_vol_template]_sub2*
[xsh] = -[xcg]
[ysh] = -[ycg]
[zsh] = -[zcg]
SYS
echo -n " Iter: {%I0%[iter]} Shift: {%F4.1%[xsh]},{%F4.1%[ysh]},{%F4.1%[zsh]}" ; date '+ Time: %x %X'
MY FL
RE
;