; Stack particles by defocus groups
;
; SOURCE: spider/docs/techs/recon/newprogsnat2stk.spi
;
; PURPOSE: Stack original particles by group, renumbering the
; original particles. Reads serially listed individual particles
; provided in the Nature Protocols paper and stacks them.
; Not used with current versions of particle picking procedures!!!
; Renames: Micrographs/raw*** -- raw****
; Renumbers: good/ngood*** -- Alignment/sel_particles_***
; NOTE: The Nature protocols data lacks info necessary to recreate the
; whole original micrograph series, only four micrographs are
; included in the data set although the windowed particles
; appear to come from 7 micrographs?, so this just
; creates defocus group stacks not micrograph stacks.
;
; ------------ Input files ---------------------------------------
[sel_micrograph] = 'sel_micrograph' ; Micrograph selection file
[microg] = 'Micrographs/raw{***[mic]}' ; Original micrograph files
[ord_sel] = 'Particles/order_select' ; Doc file listing particle series in group
[win] = 'Particles/win/ser*****' ; Individual particle images (not stacked)
; --------------- Output files -------------------------------------
[newmicrog] = '/Micrographs/raw{****[mic]}' ; Renamed Original micrographs
[sel_part_by_grp] = 'Alignment/sel_particles_***' ; Renumbered doc files of selected particle numbers
[stk] = 'Alignment/data{***[grp]}' ; Particle images stacked by group
[sel_grp] = 'Alignment/sel_group' ; Group selection doc file
; -------------- END BATCH HEADER ------------------------------
MD
TR OFF ; Decreases results file output
MD
VB OFF ; Decreases results file output
VM
echo " Results file omitted for speed" ; echo ' '
MD
RESULTS OFF ; Omits any results file output
DO ; Loop over all micrographs ----------------
UD NEXT [keym],[mic] ; Get a micrograph number
[sel_micrograph] ; Micrograph listing (input)
IF ([keym].LE.0) EXIT ; End of groups in doc file
VM ; Add digit to name
\mv [microg].$DATEXT [newmicrog].$DATEXT
VM
echo ' 'Renamed files for micrograph: {*****[mic]}
ENDDO
UD NEXT END ; Finished with this micrograph
[sel_micrograph]
VM ; Rename
\cp -p Power_Spectra/defocus.dat Power_Spectra/sel_group.dat
VM
echo ' '
DE
[sel_grp] ; Group selection doc file (output)
VM
echo ' 'Slow stacking step, please wait
[totparts] = 0
[igo] = 1
DO ; Loop over all defocus groups ----------------
UD NEXT [grp],[npart],[iend],[def] ; Get group number and ending particle number
[ord_sel]
IF ([grp].LE.0) EXIT ; End of groups in doc file
[num] = 0
!VM
!echo ' ' grp: {***[grp]} npart: {****[npart]} iend: {*****[iend]}
DE
[sel_part_by_grp][grp] ; Renumbered files of sel. particles (output)
DO [ipart]=[igo],[iend] ; Loop over all particles in this group -------------
[num] = [num] + 1
CP ; Copy particle image to output stack
[win][ipart] ; Original image for this particle (input)
[stk]@{*****[num]} ; Stacked image (output)
SD [num],[num]
[sel_part_by_grp][grp] ; Renumbered files of sel. particles (output)
ENDDO
[totparts] = [totparts] + [num]
SD [grp],[grp],[num],[def]
[sel_grp] ; Group selection doc file (output)
VM
echo ' 'Group: {***[grp]}' ' Particles: {****[num]}' ' In: [stk]
[igo]= [iend] + 1 ; Next starting number
ENDDO
UD NEXT END ; Finished with this defocus group
[ord_sel]
VM
echo ' '; echo ' 'Total particles: {*****[totparts]} ; echo ' '
EN
;