; GENERATE COORDINATES FILES FOR SELECTED PARTICLES

; ------------------- Parameter -------------------

x56 = 4  ; prints progress message to screen every (x56)th micrograph

; --------------------- Inputs ---------------------
fr l
[mic_list]../sel_micrograph                        ; micrograph-selection doc
fr l
[combined_coord_doc]../Particles/coords/sndc****   ; total coordinates doc
;fr l
;[mic2global]../Particles/coords/mic2global****    ; micrograph-slice to global-particle lookup table (optional)
fr l
[mic_good_list]../Particles/good/ngood****         ; good-particle-by-micrograph doc

; -------------------- Outputs --------------------
fr l
[good_coord_doc]../Particles/coords/good_sndc****  ; good-particle coordinates doc

; ---------------- END BATCH HEADER ----------------

fr l
[ngood_reorder]tmpngood
fr l
[unrenum_good_coords]tmpsndc

vm
echo "Generating coordinate files for good particles"; date

; initialize particle-counters
[ngood-counter] = 0
[sndc-counter]  = 0

; get #micrographs
ud n [num-mics]
[mic_list]

; loop through micrographs
do lb1 x10 = 1,[num-mics]
    ; get micrograph# (x11)
    ud ic,x10,x11
    [mic_list]
    
    if (int(x10/x56).eq.x10/x56) then
        vm
        echo "Working on micrograph {****x11}, {****x10} out of {****[num-mics]}"
    endif
    
    
    ; RE-ORDER COLUMNS IN NGOOD FILE
    
    ; delete pre-existing file
    de
    [ngood_reorder]
    
    ; get #particles
    ud n [num-parts]
    [mic_good_list]x11

    [ngood-counter] = [ngood-counter] + [num-parts]

    ; trap for no particles
    if([num-parts].eq.0) then
        vm
        touch [ngood_reorder].$DATEXT
        goto lb5
    endif

    ; loop though particles
    do lb5 x50 = 1,[num-parts]
        ; read NGOOD file
        ud ic x50,[mic-slice],x52,x53,x54
        [mic_good_list]x11
        
        ; write to temp NGOOD doc
        sd x50,x52,x53,[mic-slice],x54
        [ngood_reorder]
    lb5
    ; end particle-loop
    
    ; close docs
    ud ice
    [mic_good_list]x11
    sd e
    [ngood_reorder]
    
    ; intersect coords doc and temp NGOOD doc
    doc and
    [combined_coord_doc]x11
    [ngood_reorder]
    [unrenum_good_coords]  ; OUTPUT
    (3)                    ; column# to intersect: mic-slice
    
    ; renumber keys
    doc ren
    [unrenum_good_coords]
    [good_coord_doc]x11
    
    ; label output doc
    SD /       XCOORD       YCOORD      MICSLICE     CCCOEFF
    [good_coord_doc]x11
    sd e
    [good_coord_doc]x11

    ; count #new-particles
    ud n [num-newparts]
    [good_coord_doc]x11

    [sndc-counter] = [sndc-counter] + [num-newparts]

    ; clean up
    de
    [ngood_reorder]
    de
    [unrenum_good_coords]
lb1
; end micrograph-loop

; clean up
ud ice
[mic_list]

vm m
echo; 
echo "Done"; 
echo "Accounted for {******[sndc-counter]} out of {******[ngood-counter]} particles"; 
date
.

en d

; Modified 2009-02-24
;    TO DO: add global# if MIC2GLOBAL exists