; Repicks particles from micrographs
;
; SOURCE: Adapted from lfc_pick.spi, pickparticle.spi
;
; CALLS: convert_p.spi
; ------------- Parameters ----------------
[decimate] = 0 ; Decimation factor (0 = get value from param file)
; [decimate] = decimation factor for 'DC S' operation
; 0 = get value from param file
; 1 = full sized image
; 2 = 1/2 size
; 4 = 1/4 size
; ------------- Input files ----------------
FR G
[params]../params ; Parameter file
FR G
[sel_mic]../sel_micrograph ; Micrograph file numbers
FR G
[micgr]../Micrographs/mic{****[mic]} ; Micrograph images
FR G
[sndc]coords/sndc{****[mic]} ; Template for doc file with coordinates
FR G
[noise]../Particles/noise ; Noise file
; ------------ Output files ---------------
FR G
[ser]../Particles/win/winser_{****[mic]}@ ; Template for particle image stacks
; ------------ END BATCH HEADER ------------
MD ; Use all available processors
SET MP
0
MD ; Skip unnecessary output
VB OFF
MD ; Skip unnecessary output
TR OFF
MY FL
FR G
[out]out{****[mic]} ; Temporary spider file for converting from other formats
; Get window size & actual size from parameter file. If zero, compute them
UD 17, [windiam] ; Get window diameter
[params]
; initialize particle-counter
[part] = 0
MY FL
; Loop over all micrographs ----------------------------------------------------
DO
UD NEXT [key],[mic] ; Get micrograph number
[sel_mic]
IF ([key].LE. 0) EXIT
@convert_p([mic],[decimate])
[params] ; Parameter file
[micgr] ; Input micrograph
[out] ; Template for output SPIDER file
UD N [n] ; Get number of particles in this micrograph
[sndc]
; calculate center-to-top-left distance
X33 = INT([windiam]/2)+1
X34 = INT([windiam]/2)+1
X13 = INT([windiam]/2)-1 ; for masking radius
; MAKE A MASK FILE
MO
_26
[windiam],[windiam]
C
X13
; PIXELS THOSE ARE PART OF THE PARTICLE ARE EXCLUDED FROM NORMALIZATION
AR
_26
_28
(P1-1)*(-1)
; COPY NOISE FILE TO MEMORY
CP
[noise]
_27
; loop through particles
DO LB2 X26 = 1,[n]
UD IC,X26,X27,X28,X94,X97
[sndc]
X84 = X27 - X33
X85 = X28 - X34
WI
[out]
_29
[windiam],[windiam]
X84,X85 ; top-left coordinates
RA
_29
_22
; NORMALIZE AS PER HISTOGRAM
CE FIT
_27 ; INPUT: noise file
_22 ; INPUT: ramp-corrected windowed-image
_28 ; INPUT: inverted mask
[ser]{******X26}
LB2
UD ICE
[sndc]
[part]=[part]+[n] ; Increment the particle counter
DE ; Delete the temporary SPIDER file
[out]
VM
echo ' 'Picked: {*****x26} images from micrograph: {*****[mic]}
ENDDO
VM
echo ' 'Total picked particles: {*******[part]}
VM
echo ' '
EN D
;
; Modified 2010-09-09