; 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
[win_dir]win ; Output directory for particle image stacks
FR G
[ser][win_dir]/winser_{****[mic]}@ ; Template for particle image stacks
; ----------- END BATCH HEADER -----------
fr l
[temp_circle_mask]_26
fr l
[temp_inverted_mask]_28
fr l
[temp_noise_incore]_27
fr l
[temp_windowed]_29
fr l
[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
FR G
[out]out{****[mic]} ; Temporary spider file for converting from other formats
; Get window size from parameter file
UD 17, [windiam] ; Get window diameter
[params]
; initialize particle-counter
[part] = 0
; create directory if necessary
vm
echo "if(! -d [win_dir]) mkdir -p [win_dir]"|csh
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])
@convert_p([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
[half-xdim] = INT([windiam]/2)+1
[half-ydim] = INT([windiam]/2)+1
[mask-radius] = INT([windiam]/2)-1
; MAKE A MASK FILE
MO
[temp_circle_mask]
[windiam],[windiam]
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 LB2 [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]
[windiam],[windiam]
[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]}
LB2
UD ICE
[sndc]
[part]=[part]+[n] ; Increment the particle counter
DE ; Delete the temporary SPIDER file
[out]
VM
echo ' 'Picked: {*****[n]} images from micrograph: {*****[mic]}
ENDDO
VM
echo ' 'Total picked particles: {*******[part]}
VM
echo ' '
EN D
; Modified 2012-07-19
; 2012-07-19 (trs) -- creates output directory if needed
; 2012-05-03 (trs) -- convert_p no longer uses micrograph# as an input
;