; Create new particle selection doc files
;
; SOURCE: spider/docs/techs/recon1/Procs/number-parts.spi Jul 2013 ArDean Leith
;
; PURPOSE: Create new particle selection doc files listing the verified particle numbers.
; Optionally stores project ID, micrograph number, original window number, and
; a new global particle number in image file header.
; This procedure does NOT restack images, it just creates particle selection doc files.
;
; USAGE: clean ; spider spi/dat @number-parts
; ------------------- Parameters -------------------
[projid] = 1 ; Project id number (arbitrary)
[first-global] = 1 ; First global particle number
[max-particles] = 0 ; Max number of particles/micrograph (0 == keep all)
[labelheader-yn] = 1 ; Put label in the image header? (0 == no)
; --------------------- Inputs ---------------------
[sel_micrograph] = '../sel_micrograph' ; Micrograph selection list (one)
;[old_sel_part] = 'win/sel_part_****' ; Original particle selection files (one/micrograph)
[old_sel_part] = 'win/sel_good_****' ; Visually picked particle selection files (one/micrograph)
[win_stacks] = 'win/data_bymic_****' ; OPTIONAL Micrograph stacks (Used if labelling image header)
; --------------------- Output ---------------------
[good_dir] = 'good' ; New selection doc files directory (one)
[new_sel_part] = '[good_dir]/sel_part_****' ; Particle selection doc files (one/micrograph)
[micwin2global] = 'win/micwin2glonum_****' ; Global particle lookup tables (one/micrograph)
[global2micwin] = 'win/glonum2micwin' ; Global particle lookup tables (one)
[summary_doc] = 'percent_selected' ; Summary doc file (one)
; ---------------- END BATCH HEADER ----------------
; Temporary file
[temp_old_doc_nodupes] = 'tmpgood_nodupes'
DE ; Clean up pre-existing file
[summary_doc] ; Doc file (removed)
SD / MIC_NUM KEPT_PARTS TOTAL_PARTS %_KEPT
[summary_doc] ; Doc file (output)
DE ; Clean up pre-existing file
[global2micwin] ; Doc file (removed)
SD / KEY: GLOBAL_NUM REG: MIC-NUM MIC-WIN
[global2micwin] ; Global particle lookup table (output)
; Initialize global-particle counter
[global-num] = [first-global] - 1
IF ( [labelheader-yn] >= 1) THEN
SYS
echo " Placing global particle # in image header" ; echo
ELSE
SYS
echo " Not placing global particle # in image header" ; echo
ENDIF
SYS ; Create directory if needed
mkdir -p [good_dir]
; Get number of micrographs
UD N [num-mics] ; Get number
[sel_micrograph] ; Doc file (input)
DO [mic-key]=1,[num-mics] ; Loop over all all micrographs ----------
UD IC [mic-key], [mic] ; Get micrograph number
[sel_micrograph] ; Micrograph selection file (input)
; Delete pre-existing files and label new files
DE
[micwin2global][mic] ; Doc file (removed)
; Label for new global number doc file
SD / KEY: WIN_NUM REG: GLOBAL-NUM MICROGRAPH
[micwin2global][mic] ; Doc file (output)
DE
[new_sel_part][mic] ; Doc file (removed)
SD / WIN MIC_WIN MIC GLOBAL_NUM GRP
[new_sel_part][mic] ; Doc file (output)
; Get number of particles including duplicates
UD N [tot-parts]
[old_sel_part][mic] ; Doc file (input)
; Remove duplicates and sort
AT IT ; Sort doc file
[old_sel_part][mic] ; Doc file (input)
[temp_old_doc_nodupes] ; Doc file (output)
; Get # particles kept
UD N [num-particles] ; Get # particles
[temp_old_doc_nodupes] ; Doc file (input)
; Limit # particles/micrograph if desired
IF ([max-particles] > 0) THEN
IF ( [num-particles] > [max-particles] ) [num-particles] = [max-particles]
ENDIF
; Loop through all particles for this micrograph --------------------
DO [p-key] = 1,[num-particles]
; Read micrograph window #
UD IC [p-key], [win]
[temp_old_doc_nodupes] ; Doc file (input) ;
; Increment global #
[global-num] = [global-num] + 1
; Write global # micrograph to global-particle lookup table
SD [p-key], [global-num], [mic]
[micwin2global][mic] ; Doc file (output)
SD [global-num],[mic],[win]
[global2micwin] ; Global particle lookup table (output)
; Write details to particle selection file
SD [p-key],[p-key],[win],[mic],[global-num], [mic]
[new_sel_part][mic] ; Doc file (output)
IF ( [labelheader-yn] >= 1 ) THEN
; Put global # into image header
ST H ; Set header values
[win_stacks]@****[mic][p-key] ; Image file (input)
PROJ,MIC,NUM,GLONUM ; Header locations
[projid],[mic],[win],[global-num] ; Values
ENDIF
ENDDO ; End particle-loop
; Close docs
UD ICE ; Close document file
[temp_old_doc_nodupes] ; Doc file (closed)
SD E ; Close document file
[micwin2global][mic] ; Doc file (closed)
SD E ; Close document file
[new_sel_part][mic] ; Doc file (closed)
DE ; Delete document file
[temp_old_doc_nodupes] ; Doc file (removed)
; Count # of particles
UD N [kept] ; Get # of particles
[new_sel_part][mic] ; Doc file (input)
SYS
echo " Kept: {%I6%[kept]} particles from micrograph: {%I4%[mic]}"
[percent-kept] = 100 * [kept]/[tot-parts]
; Maybe should trap for zero someday
; Write to summary doc
SD [mic-key], [mic],[kept],[tot-parts],[percent-kept]
[summary_doc] ; Doc file (output)
ENDDO ; End micrograph loop
UD ICE ; Close document file
[sel_micrograph] ; Doc file (closed)
SD / MICROGRAPHS TOTAL_PARTS
[summary_doc] ; Doc file (output)
SD -1, [num-mics],[global-num]
[summary_doc] ; Doc file (output)
SD E ; Close document file
[summary_doc] ; Doc file (output)
SD E ; Close document file
[global2micwin] ; Doc file (closed)
SYS
echo ; echo " Kept: {%I0%[global-num]} particles from: {%I0%[num-mics]} micrographs" ; echo
EN
; Modified 2013-10-26
; 2013-10-26 (agl) -- Added current group col. to particle selection files
; 2013-10-16 (agl) -- Syntax modernized, file names changed
; 2012-07-19 (trs) -- Creates output directory if needed
; 2012-05-01 (trs) -- Optionally writes global particle number to header position 42
; 2012-04-05 (trs) -- Doesn't use output from pnums.spi anymore
; 2012-04-05 (trs) -- Adapted from listallparticles.spi
; 2010-09-02 (trs & ay) -- Trap for >999 micrographs for 'SD [dummy]' line
; 2009-10-16 (trs) -- Removed option for unstacked images
; 2008-10-03 (trs) -- Added output file micwin2global
; 2008-10-03 (trs) -- Assigns global particle number
; 2007-12-17 (trs) -- Optional parameter for maximum number of particles per micrograph
; 2007-10-10 (trs) -- Gets number of micrographs from SEL_MICROGRAPH
;