; Pick particles from micrographs
;
; PURPOSE: Uses local fast correlation algorithm to pick particles from
; input micrographs. Requires a reference volume.
;
; SOURCE: spider/docs/techs/recon1/Procs/pick-lfc.spi
;
; REQUIRES: convert-p.spi & pick-lfc-p.spi
;
; USAGE: clean ; spider spi/dat @pick-lfc
[firstPart] = 1 ; First particle number (e.g., 1 or next particle number)
[numMics] = -1 ; Number of micrographs (useful for testing, -1 == All)
; [decimate] = 0 ; Decimation factor (0 = get value from param file)
; ; 0 = get value from param file
; ; 1 = full sized image
; ; 2 = 1/2 size
; ; 4 = 1/4 size
![ccthresh] = 0.061 ; CC threshold for particles to be windowed (-1 == All)
[ccthresh] = 0.0 ; CC threshold for particles to be windowed (-1 == All)
; Correlations can be negative
[sep] = 0.62 ; Separation distance (fraction of window size) al feb 2007
; Peak separation distance (e.g., 75% of window size) may be changed such
; that [sep]*[sp_winsiz] ~ size of particle, where [sp_winsiz]= side of the window
[useSelectYN] = 0 ; Use Euler angle doc file? (0 == No, 1 == Yes)
; If No, projections will be computed from angle start/end/step set below
[phiStart] = 0 ; Starting phi (unused with selection file)
[phiEnd] = 0 ; Ending phi (unused with selection file)
[phiStep] = 0 ; Phi increment (unused with selection file)
[thetaStart] = 0 ; Starting theta (unused with selection file)
[thetaEnd] = 0 ; Ending theta (unused with selection file)
[thetaStep] = 0 ; Theta increment (unused with selection file)
[psiStart] = 0 ; Starting psi (unused with selection file)
[psiEnd] = 0 ; Ending psi (unused with selection file)
[psiStep] = 0 ; Psi increment (unused with selection file)
[useAvgYN] = 0 ; Use average projection? (1 == Yes, only with Euler angle doc)
[shrink] = 2 ; Interpolation factor (for speed only, doesn't shrink outputs)
[peaks] = 20000 ; Number of peaks to search
; In case of a large number, the separation-distance parameter or CC threshold will be limiting
[symmMaskYN] = 1 ; Use a circular mask? (for local st.dev. calculation)
[maskThresh] = 0 ; Masking threshold (if not using a circular mask)
[numProcs] = 0 ; Number of processors to use (0 == All)
; ----------- Input files --------------
[params] = '../params' ; Parameter file (one)
[sel_mic] = '../sel_micrograph' ; Micrograph file numbers (one)
[micgr] = '../Micrographs/raw{****[mic]}' ; Raw micrograph images (one / micrograph)
[refvol] = '../reference_volume' ; Reference volume (one / micrograph)
[noise] = 'noise' ; Noise file
[angles_doc] = '../Alignment/refangles' ; (Optional) Euler angle doc (one)
; ----------- Output files --------------
[win_dir] = 'win' ; Directory for particle images
[coor_dir] = 'coords' ; Directory for coordinates
[ser] = '[win_dir]/data_bymic_{****[mic]}@' ; Particle image stacks (one / micrograph)
[sel_doc] = '[win_dir]/sel_part_{****[mic]}' ; Particle selection doc files (one / micrograph)
[sndc] = '[coor_dir]/pkcoor_{****[mic]}' ; Particle center coordinates doc files (one / micrograph)
[summary_doc] = 'summary-pick-lfc' ; Summary doc file
; -------------- END BATCH HEADER --------------------------
MD
SET MP
[numProcs]
MD ; Avoid memory over-allocation for large images
SET THREADS
1
MD ; Skip unnecessary output
VB OFF
MD ; Skip unnecessary output
TR OFF
MY FL
UD 5, [sp_pixsiz] ; Get pixelsize
[params]
; Get window size from parameter file. If zero, compute
UD 17, [sp_winsiz] ; Get window diameter
[params]
; For ribosomes, actual size = 250 A, window = 368 A
IF ( [sp_winsiz] < 1 ) [sp_winsiz] = INT(368/[sp_pixsiz])
; Compute peak separation distance ([sep] is x% of window size)
[peaksep] = [sep] * [sp_winsiz]
[peaksep] ; Echo to results file
; Create directories if necessary
SYS
mkdir -p [win_dir]
SYS
mkdir -p [coor_dir]
DE
[summary_doc]
SD / MIC_NUM NUM_PARTS NUM_PEAKS
[summary_doc]
MY FL
[part] = [part] - 1
DO ; Loop over all micrographs ------------------
UD NEXT [key],[mic] ; Get micrograph number
[sel_mic]
IF ([key] <= 0) EXIT
DE
[sndc] ; Delete any old output document files
@pick-lfc-p([numPeaks],[pickedParts])
[micgr] ; Input micrograph
[refvol] ; Reference volume (input)
[noise] ; Noise image for normalization of particles
[ser] ; Template for windowed particles (output)
[firstPart] ; Starting particle number
[sndc] ; Doc file with particle co-ordinates (output)
[useSelectYN] ; Use selection file
[angles_doc] ; Selection file (input)
[useAvgYN] ; Use average projection? (with selection file only)
[phiStart] ; PHI start value (unused with selection file)
[phiEnd] ; PHI end value (unused with selection file)
[phiStep] ; PHI step size (unused with selection file)
[thetaStart] ; THETA start value (unused with selection file)
[thetaEnd] ; THETA end value (unused with selection file)
[thetaStep] ; THETA step size (unused with selection file)
[psiStart] ; PSI start value (unused with selection file)
[psiEnd] ; PSI end value (unused with selection file)
[psiStep] ; PSI step size (unused with selection file)
[shrink] ; Interpolation factor
[peaks] ; No of peaks to be searched (arbitrary)
[peaksep] ; Peak separation distance
[symmMaskYN] ; Use symmetric mask? (0 == no)
[maskThresh] ; Pixel threshold for asymmetric mask (unused for symmetric mask)
[ccthresh] ; Threshold for CC peaks
UD N [n] ; Get number of particles in this micrograph
[sndc]
[part] = [part]+[n] ; Increment the particle counter
SYS
echo ' 'Picked {%I0%[pickedParts]} images out of {%I0%[numPeaks]} peaks from: [micgr]; echo
SD [key], [mic],[pickedParts],[numPeaks]
[summary_doc]
DOC CREATE ; Make selection doc file
[sel_doc] ; Doc file (output)
1 ; First register
1-[n] ; Image numbers
[micCounter] = [key]
; ([key] will be reset to 0 when loop is complete)
IF ([micCounter] == [numMics]) EXIT
ENDDO
[dummy] = -[micCounter]
SD [dummy], [part]
[summary_doc]
SD / MIC PARTS
[summary_doc]
SD E
[summary_doc]
SYS
echo ' 'Total picked particles: {%I0%[part]} from {%I0%[micCounter]} micrographs; echo ' '
EN
; Modified 2016-02-05
; 2016-02-05 (trs) -- Added peak CC threshold
; 2016-02-03 (trs) -- No longer converts micrograph, should be SPIDER format already
;