; Normalizes stacks and creates star file
;
; PURPOSE: Normalizes groups of spider stacks and creates 'star' file for Relion.
;
; SOURCE: norm_n_star.spi
;
; USAGE: spider spi/dat @norm_n_star
[id] = '1' ; New stack id letter
; -------- Adjust these parameters for your project ----------- EDIT -----
[DefAng] = 0 ; Defocus angle from 'params.spi' file (degrees)
[Volt] = 200 ; Electron voltage from 'params.spi' file (KV)
[ACR] = 0.1 ; Amplitude Contrast Ratio from 'params.spi' file
[SphAb] = 2 ; Spherical Aberration from 'params.spi' file
; ------------------ Input files -----------------------
[sel_grp] = 'sel_group' ; Group selection file
[sel_part] = 'Alignment/sel_particles_{***[grp]}' ; Particle selection files (one/group)
[part] = 'Alignment/data{***[grp]}' ; Particle stacks (one/group)
; ----------------- Output files -----------------------
[id] = '1' ; New stack id letter
[starfile] = 'relion_[id]_data.star' ; New star files (one)
[norm_part] = 'input/data_norm_{***[grp]}' ; New particle stacks (one / group)
; -------------- END BATCH HEADER -------------------------------
[select] = '{*****[n]}@[norm_part]'
MD
VB OFF
SYS
\rm [starfile]
SYS
echo data_ >> [starfile]
SYS
echo loop_ >> [starfile]
SYS
echo _rlnImageName >> [starfile]
SYS
echo _rlnDefocusU >> [starfile]
SYS
echo _rlnDefocusV >> [starfile]
SYS
echo _rlnDefocusAngle >> [starfile]
SYS
echo _rlnVoltage >> [starfile]
SYS
echo _rlnAmplitudeContrast >> [starfile]
SYS
echo _rlnSphericalAberration >> [starfile]
[ngrps] = 0
[ntot] = 0
DO ; Loop over all groups -------------------
UD NEXT [key], [grp],[np],[Def] ; Get input group number
[sel_grp] ; Group selection doc file (input)
IF ( [key] <= 0 ) EXIT
SYS
echo " Group: {%I3%[grp]} Images: {%I5%[np]} Defocus: {%I5%[Def]}"
[ntot] = [ntot] + [np]
[ngrps] = [ngrps] + 1
NORM ; Normalize image contrast
[part]@* ; Spider stack file (input)
[sel_part] ; Selection file (input)
* ; No mask file
[norm_part]@* ; Spider stack file (output)
N ; No flat field
DO ; Loop over all particles ------------
UD NEXT [key], [n] ; Get input image number
[sel_part] ; Selection file (input)
IF ( [key] <= 0 ) EXIT
SYS
echo [select].spi {*****[Def]} {*****[Def]} {%f6.2%[DefAng]} {%i4%[Volt]} {%f5.2%[ACR]} {%f5.1%[SphAb]} >> [starfile]
!echo [select].spi {*****[Def]} {*****[Def]} 0.0 200 0.1 2.00 >> [starfile]
ENDDO ; End loop over all particles --------
UD NEXT E ; Get input image number
[sel_part] ; Selection file (input)
ENDDO ; End loop over all groups ---------------
UD NEXT E ; Get input image number
[sel_grp] ; Group selection doc file (input)
SYS
echo " Groups: {%I0%[ngrps]} Images: {%I0%[ntot]} "
EN
! ------------------------ UNUSED BELOW HERE ------------------------------
FS
[part]@2 ; Spider stack file (input)
FS
[norm_part]@2 ; Spider stack file (input)