([freq],[iter],[ampenhance])
;
; Merges groups at end of each refinement iteration
;
; SOURCE: mergegroups.pam ArDean Leith Nov 2000
; saveresp Jan 2005
; enhance Apr 2005
; [] Dec 2005
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/programs/
;
; PURPOSE: Consolidates CTF data at end of each iteration, not in ||
;
; CALLED FROM: pub_refine pub_refine.pam
;
; INPUT REGISTERS:
; [freq] Nyquist frequency
; [iter] Refinement step iteration counter
; [ampenhance] Flag to use amplitude enhancement
;
; INPUT FILES:
; input/order_select_sort [sorted_order_select]
; work/ctf*** [temp_ctf_file_template] Template for 3D CTF files
; work/defgrp{***grp}/vol{**iter} [next_group_vol]
; work/defgrp{***grp}/vol_{**iter} [next_group_vol_template] (deleted at end)
; work/defgrp{***grp}/vol_{**iter}_odd [next_group_vol_template]_odd (deleted at end)
; work/defgrp{***grp}/vol_{**iter}_even [next_group_vol_template]_even (deleted at end)
; input/mask [mask] (Mask created from input file)
; OUTPUT FILES:
; final/val{**iter} [next_val] (Unfiltered volume)
; final/vol{**iter} [next_vol] (Filtered volume)
; final/vol{**iter}_odd [next_vol]_odd (Filtered volume)
; final/vol{**iter}_even [next_vol]_even (Filtered volume)
; final/dres{**iter} [next_dres] (Resolution doc)
; work/enhance_doc ??? [enhance_doc] (enhancement document)
; ??? [next_val]_amps (amplitude-enhanced volume, unfiltered)
;
;.......................................................................
; All defocus groups must be present here for "TF CTS" use!
[ring] = 0.5 ; FSC ring width
[next-iter]=[iter] + 1 ; Next iteration
TF CTS ; Transfer Function - CTF correction
[next_group_vol_template] ; Template for 3D volumes (input)
[sorted_order_select] ; Group Selection File (input)
[temp_ctf_file_template] ; Template for 3D ctf file - work/ctf (input)
(3) ; SNR
[next_val] ; Unfiltered CTF'd volume (output)
TF CTS ; Transfer Function - CTF correction
[next_group_vol_template]_odd ; Template for 3D odd volumes (input)
[sorted_order_select] ; Group Selection File (input)
[temp_ctf_file_template] ; Template for 3D ctf files - work/ctf (input)
(3) ; SNR
[next_vol]_odd ; Odd volume (output)
TF CTS ; Transfer Function - CTF correction
[next_group_vol_template]_even ; Template for 3D even volumes (input)
[sorted_order_select] ; Group Selection File (input)
[temp_ctf_file_template] ; Template for 3D ctf files - work/ctf (input)
(3) ; SNR
[next_vol]_even ; Even output volume (output)
DE
[next_dres] ; Resolution output doc file
; Resolution calculation
RF 3 [p69],[spfreq] ; Phase Residual & Fourier shell correlation
[next_vol]_odd ; Odd volume (input)
[next_vol]_even ; Even volume (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] ; Resolution doc file - dres_iter (output)
[grp] = 0 ; Defocus group is zero now (none)
@saveresp([freq],[iter],[grp],[spfreq]) ; Record resolution in doc file
[dbpr_resol] ; Output file (output)
IF ([spfreq] .GT. 0.35) [spfreq] = 0.4 ; Limits pass-band
[stop-band]= [spfreq]+0.15 ; Stop band frequency
[filter-limit]=int([p69]*[ring]) ; Filter limit
[filter-limit] ; diagnostic
IF ([ampenhance] .EQ. 1) THEN ; Use amplitude enhancement
DE ; Delete
[enhance_doc] ; Output enhancement document file
; Generate amplitude enhancement curve
@enhance([filter-limit],[freq],[next-iter]) ; Filter limit, Max. spatial frequency, Next iter.
[next_val] ; Input volume
FD ; Filter using enhancement doc. file
[next_val] ; Input volume
[next_val]_amps ; Output amplitude-enhanced volume, unfiltered
[enhance_doc] ; Input enhancement document file
FQ ; Quick Filter
[next_val]_amps ; Input file (Created above) - val
[next_vol] ; Output volume, ampl enhanced and filtered
(7) ; Butterworth low pass filter
[spfreq],[stop-band] ; Pass-band and stop-band frequency
IQ FI [masked] ; See if mask file exists
[mask] ; Mask created from ribosome-translocon
IF ([masked] .GE. 1) THEN ; Use mask file
MM C ; Mask multiply to eliminate high freq. noise
[mask] ; Mask created from ribosome-translocon
[next_vol] ; Volume for next iteration
ENDIF
ELSE
; Filter output volume to limit the resolution
FQ ; Quick Filter
[next_val] ; Input file (Created above) - val
[next_vol] ; Creates filtered volume, used on next iter.
(7) ; Butterworth Low pass filter
[spfreq],[stop-band] ; Pass-band and stop-band frequency
ENDIF
VM ; Saves space for tests - grp/vol!.
\rm [next_group_vol_template]_odd* [next_group_vol_template]_even*
VM
echo " Merged groups for iteration: {**[iter]}"
VM
date '+ Time: %x %X'
MY FL
RE
;