; Repicks particles from micrographs
;
; SOURCE: spider/docs/techs/recon1/Procs/rewindow.spi
;
; ORIGIN: Adapted from lfc_pick.spi, pickparticle.spi
;
; PURPOSE: Repicks particles from micrographs
;
; REQUIRES: convert-p.spi
;
; USAGE: clean ; spider spi/mrf @rewindow
; ----------- Parameters --------------
[deci] = 0 ; Decimation factor (0 = get value from param file)
; [deci] = 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 --------------
[params] = '../params' ; Parameter file (one)
[sel_mic] = '../sel_micrograph' ; Micrograph selection doc file (one)
[micgr] = '../Micrographs/mic{****[mic]}' ; Micrograph images
![sndc] = 'coords/sndc_{****[mic]}' ; Window center coordinates doc file
[sndc] = 'coords/pkcoor_{****[mic]}' ; Window center coordinates doc file
[noise] = '../Particles/noise' ; Noise file (one)
; ----------- Output files --------------
[win_dir] = 'win' ; Output directory for particle images
![ser] = '[win_dir]/winser_{****[mic]}@' ; Particle image stacks
[ser] = '[win_dir]/data_bymic_{****[mic]}@' ; Particle image stacks
; ----------- END BATCH HEADER -----------
[temp_circle_mask] = '_26'
[temp_inverted_mask] = '_28'
[temp_noise_incore] = '_27'
[temp_windowed] = '_29'
[temp_ramp_corrected] = '_22'
MD ; Use all available processors
SET MP
0
MD ; Skip unnecessary output
VB OFF
MD ; Skip unnecessary output
TR OFF
MY FL
[out] = 'out{****[mic]}' ; Temp. SPIDER file for conversions
; Get window size from parameter file
UD 17, [sp_winsiz] ; Get window size
[params]
; Calculate center-to-top-left distance
[half-xdim] = INT([sp_winsiz]/2)+1
[half-ydim] = INT([sp_winsiz]/2)+1
[mask-radius] = INT([sp_winsiz]/2)-1
; Initialize particle-counter
[part] = 0
; Create directory if necessary
SYS
echo mkdir -p [win_dir]
MY FL
; Loop over all micrographs ----------------------------------------------------
DO
UD NEXT [key],[mic] ; Get micrograph number
[sel_mic]
IF ( [key] <= 0 ) EXIT
@convert-p([deci])
[params] ; Parameter file
[micgr] ; Input micrograph
[out] ; Template for output SPIDER file
UD N [n] ; Get number of particles in this micrograph
[sndc]
; Make a mask file
MO
[temp_circle_mask]
[sp_winsiz],[sp_winsiz]
C
[mask-radius]
; Pixels those are part of the particle are excluded from normalization
AR
[temp_circle_mask]
[temp_inverted_mask]
(P1-1)*(-1)
; Copy noise file to memory
CP
[noise]
[temp_noise_incore]
; Loop through particles
DO [part-key] = 1,[n]
; read x-coord, y-coord
UD IC [part-key], [xcenter],[ycenter] ; [mic-slice],[peak-height] ; (last 2 not used)
[sndc]
[x-topleft] = [xcenter] - [half-xdim]
[y-topleft] = [ycenter] - [half-ydim]
WI
[out]
[temp_windowed]
[sp_winsiz],[sp_winsiz]
[x-topleft],[y-topleft] ; Top-left coordinates
RA
[temp_windowed]
[temp_ramp_corrected]
; Normalize as per histogram
CE FIT
[temp_noise_incore] ; (input)
[temp_ramp_corrected] ; (input)
[temp_inverted_mask] ; (input)
[ser]{******[part-key]}
ENDDO
UD ICE
[sndc]
[part] = [part]+[n] ; Increment the particle counter
DE ; Delete the temporary SPIDER file
[out]
SYS
echo ' 'Picked: {%I5%[n]} images from micrograph: {%I5%[mic]}
ENDDO
SYS
echo ' 'Total picked particles: {%I0%[part]}; echo ' '
EN D
; Modified 2013-10-16
; 2013-10-16 (agl) -- modernized
; 2012-07-19 (trs) -- creates output directory if needed
; 2012-05-03 (trs) -- convert-p no longer uses micrograph# as an input
;