; Normalizes stacks and creates star file
;
; PURPOSE: Converts Relion data 'star' file into set of SPIDER alignment files.
; SOURCE: relion_star_to_align.spi
; USAGE: spider spi/dat @relion_star_to_align
;
; POSSIBLE COLUMNS CORRESPONDING TO STANDARD RELION STAR DATA DESCRIPTORS
; _rlnImageName #7 Image name sometimes contains 2 integer strings for image
; _rlnOriginX #12 X-shift
; _rlnOriginY #13 Y-shift
; _rlnAngleRot #9 Rot
; _rlnAngleTilt #10 Tilt
; _rlnAnglePsi #11 Psi
; _rlnClassNumber #14 Class #
;
; ----------------- Variables -----------------------
! No need to alter these variables when using standard Relion data files
[star_vars] = '_rlnOriginX,_rlnOriginY,_rlnAngleRot,_rlnAngleTilt,_rlnAnglePsi,_rlnClassNumber'
[star_img_name] = '_rlnImageName'
[iter] = 10 ; Set Relion iteration number
; ------------------ Input files -----------------------
[indir] = '.'
[star] = '[indir]/classify_it{***[iter]}_data.star' ; Star iteration data file (one)
; ----------------- Output files -----------------------
[outdir] = 'input'
[star_doc] = '[outdir]/star_doc_{**[iter]}' ; Temp doc file without alphabetical chars (one)
[align_doc] = '[outdir]/ali_doc' ; Overall alignment file (one)
[align_grp_doc] = '[outdir]/ali_doc_***' ; Group alignment file (one/group)
[sel_grp] = '[outdir]/sel_grp' ; Group selection file (one)
[sel_part] = '[outdir]/sel_part_{**[grp]}' ; Particle selection file (one/group)
! Unused examples for use with Relion classified data
![class] = 4 ; Image class desired
![star] = '[indir]/class{*[class]}_only_it{***[iter]}_input.star' ; Star class data file (one)
![align_doc] = '[outdir]/ali_doc_{**[class]}' ; Class alignment file (one)
![align_grp_doc] = '[outdir]/ali_doc_{**[class]}_***' ; Group alignment file (one/group)
; -------------- END BATCH HEADER -------------------------------
MD
VB OFF ; Decrease results file output
DE ; Delete existing output file
[star_doc]
DE ; Delete existing output file
[align]
; Convert Relion 'star' file into a temporary SPIDER doc file ------------------
; Need to import: [n],[grp], [xsh],[ysh],[s_rot],[s_tilt],[s_psi],[class]
; From: '_rlnOriginX,_rlnOriginY,_rlnAngleRot,_rlnAngleTilt,_rlnAnglePsi,_rlnClassNumber'
XM S2D [nkeys) ; Convert star file to doc file
[star] ; Star file (input)
[star_vars] ; Star variables wanted
3,4,5,6,7,8 ; SPIDER doc file registers
[star_img_name] ; Star file name variables wanted
1,2 ; Spider doc file registers from name
[star_doc] ; Spider doc file (output)
SYS
head [star_doc].*
; Initialize unused alignment file variables
[PSI] = 0
[REF] = 0
[DIFF] = 0
[CCROT] = 0
[ROTT] = 0
[SXT] = 0
[SYT] = 0
[MIR-CC] = 0
; Loop over all doc file lines originating from star file ------------------
DO
; Get input line from star file
UD NEXT [key], [n],[grp], [xsh],[ysh],[s_rot],[s_tilt],[s_psi],[class]
[star_doc] ; Spider star doc file (input)
IF ( [key] <= 0 ) EXIT
; Only want one specified class from the star file
!IF ( [class] .NE. [class] ) CYCLE
; Set alignment doc file values
[KEY] = [n] ; Will have duplicates of keys!
[EXP] = [n] ; Exp. image number
[GRP] = [grp] ; Exp image group
[THE] = [s_tilt] ; Projection angle: theta
[PHI] = [s_rot] ; Projection angle: phi
[ROT] = -[s_psi] ; RTSQ rot with PSI = 0 & matrix inversion shifts
; Matrix inversion needed since: rotate then shift in SPIDER is opposite Relion's
[SX] = [xsh] ;
[SY] = [ysh] ;
[ROT] = 0 ;
[PSI] = [s_psi] ;
SD [KEY],[PSI],[THE],[PHI],[REF],[EXP],[ROT],[SX],[SY],[GRP],[DIFF],[CCROT],[ROTT],[SXT],[SYT],[MIR-CC]
[align_doc]
ENDDO
UD NEXT E ; End alignment doc file construction
[align_doc] ; Doc file (closed)
!SYS
!cat [align_doc].*
; Separate the alignment file by group into multiple doc files -------------------------------
DOC SEP [maxgrp]
[align_doc] ; Doc file (input)
9 ; Register for separation = group number
[align_grp_doc] ; Group align doc file template (output)
KEY PSI, THE, PHI, REF#, EXP#, CUM. ROT, SX, SY, GRP, DIFF, CCROT, ROT, SX, SY, MIR-CC ; Doc file header'
[sel_grp] ; Group selection file
; Renumber keys of the group alignment doc files --------------------------------------------
DO [grp] = 1,[maxgrp]
IQ FI [ex]
[align_grp_doc][grp] ; Group align doc file template (input)
IF ( [ex] > 0 ) THEN
; Consecutively renumber doc file keys & move original key to the first register --------
DOC KEY ONE
[align_grp_doc][grp] ; Group align doc file (input)
[sel_part] ; Particle selection doc file (input)
!SYS
! cat [sel_part].$DATEXT
ENDIF
ENDDO
EN