; SEPARATES GOOD PARTICLES BY MICROGRAPH

; ---------------------------- Inputs ----------------------------
fr l
[df_good_list]../Reconstruction/df{***[df-group]}/goodparticles  ; good-particle list, for each defocus group
;        DF_SLICE   GLOBAL_PART     CC_ROT
;          used        used
fr l
[def_avg]../Power_Spectra/def_avg                                ; doc file with defocus-group for each micrograph
;       MICROGRAPH    DEFOCUS      DF_GROUP    AVGDEFOCUS
;          used                      used
fr l
[tot_particle_list]../../../Particles/coords/mic2global****      ; file pattern for list of all particles, for each micrograph
; KEY=MIC_SLICE /  GLOBAL_PART
;        used         used

; --------------------------- Outputs ----------------------------
fr l
[good_dir]../Reconstruction/Bymic  ; directory where output files will go
fr l
[mic_good_list]ngood****           ; good-particle list, for each micrograph, in GOOD_DIR
;        MICSLICE     DF_GROUP     DF_SLICE    GLOBAL_PART    CC_ROT
fr l
[mismatch_doc]docmismatch          ; doc file written if MIC2GLOBAL and GOODPARTICLES disagree

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

fr l
[temp_rekeyed_mic2global]tmp_mic2global
fr l
[temp_good_mic2global]tmp_goodmic2global
fr l
[temp_selbymic]tmp_micsel
fr l
[temp_mic_good_list]tmp_ngood

de  ; delete pre-existing file
[mismatch_doc]

vm
echo "Making good-particle list for each micrograph"; date

vm
echo "if(! -d [good_dir]) mkdir -p [good_dir]"|csh

;; get number of good particles (x83)
;ud n,x83
;[df_good_list]

; initialize particle-counters
[output-counter] = 0
[bad-counter]    = 0

; get number of micrographs (x76)
ud n,x76
[def_avg]

; loop through micrographs
do lb7 x70=1,x76
    ; get micrograph# (x71), defocus-group#
    ud ic,x70,x71,x72,[df-group]
    [def_avg]

    ; shift particle# to 2nd column
    doc key
    [tot_particle_list]x71
    [temp_rekeyed_mic2global]

    ; find union of micrograph-particle list and combined-good list
    doc and
    [temp_rekeyed_mic2global]
    [df_good_list]
    [temp_good_mic2global]
    (2)  ; column# to check: particle#
    ; DF_GOOD_LIST label contains [DF-GROUP]
    ; This sequence of inputs only shows mic-slice# and global-particle#.

    ; find union of micrograph-particle list and combined-good list
    doc and
    [df_good_list]
    [temp_rekeyed_mic2global]
    [temp_selbymic]
    (2)  ; column# to check: particle#
    ; DF_GOOD_LIST label contains [DF-GROUP]
    ; This sequence of inputs show everything in the DF_GOOD_LIST

     ; renumber keys
    doc ren
    [temp_good_mic2global]
    [temp_good_mic2global]
    doc ren
    [temp_selbymic]
    [temp_selbymic]

    ; delete pre-existing outputs
    de
    [good_dir]/[mic_good_list]x71

    ; initialize
    [good-counter]=0

    ; get #particles
    ud n [num-particles]
    [temp_good_mic2global]

    ; skip if empty
    if([num-particles].eq.0) then
        vm
        echo "Micrograph {*****x71}: Kept 0 particles"
        goto lb7
    endif

    ; allocate in-core doc file
    sd ic new
    [temp_mic_good_list]
    (5,[num-particles])  ; #columns, #rows
;    (7,[num-particles])  ; #columns, #rows

    ; loop through particles
    do lb5 x50=1,[num-particles]
        ; read from mic2global doc
        ud ic x50,[mic-slice],[global-num]
        [temp_good_mic2global]

        ; read from selbymic doc
;        ud ic x50,[view-slice],[global-num-check],[df-slice],[ccrot],[mirror],[df-group],[view-num]
        ud ic x50, [df-slice],[global-num-check],[ccrot]
        [temp_selbymic]

        ; check if no mismatch
        if([global-num].eq.[global-num-check]) then
            [good-counter] = [good-counter]+1  ; increment good-counter

            ; write to output doc
;            sd ic [good-counter],[mic-slice],[df-group],[df-slice],[view-num],[view-slice],[ccrot],[mirror]
            sd ic [good-counter], [mic-slice],[df-group],[df-slice],[global-num],[ccrot]
            [temp_mic_good_list]  ; WAS [good_dir]/[mic_good_list]x71
        else
            [bad-counter] = [bad-counter]+1  ; increment bad-counter

;            sd [bad-counter],x71,[mic-slice],[df-group],[df-slice],[view-num],[view-slice],[ccrot],[mirror]
            sd [bad-counter],x71,[mic-slice],[df-group],[df-slice],[global-num],[ccrot]
            [mismatch_doc]
            ; x71==micrograph#
        endif
    lb5
    ; end particle-loop

    [output-counter] = [output-counter]+[good-counter]

;    ; get number of good particles
;    ud n,[good-counter]
;    [good_dir]/[mic_good_list]x71

    vm
    echo "Micrograph {*****x71}: Kept {****[good-counter]} particles"

    ; clean up
    ud ice
    [temp_good_mic2global]
    ud ice
    [temp_selbymic]
    sd ic copy
    [temp_mic_good_list]
    [good_dir]/[mic_good_list]x71
    sd ic e
    [temp_mic_good_list]
;    SD /      MICSLICE     DF_GROUP     DF_SLICE      VIEWNUM    VIEW_SLICE     CCROT        MIRROR
    SD /      MICSLICE     DF_GROUP     DF_SLICE    GLOBAL_PART    CC_ROT
    [good_dir]/[mic_good_list]x71
    sd e
    [good_dir]/[mic_good_list]x71
    de
    [temp_rekeyed_mic2global]
    de
    [temp_good_mic2global]
    de
    [temp_selbymic]
lb7
; end micrograph loop

vm
echo ; echo "Total particles sorted by micrograph: {******[output-counter]}"

ud ice  ; close document
[def_avg]

sd e
[mismatch_doc]
iq fi [mismatch-exists]
[mismatch_doc]

if([mismatch-exists].eq.1) then
    ud n [num-mismatch]
    [mismatch_doc]

    vm
    echo "WARNING: Found {******[num-mismatch]} mismatches -- Check file [mismatch_doc].$DATEXT"
endif

vm
echo "Done"; date

en d

; Modified 2011-01-11
;    2011-01-11 (trs) -- uses DF/GOODPARTICLES and DEF_AVG instead of COMBINEDGOOD, for speed
;    2008-12-30 (trs) -- added information to output file
;    2008-11-19 (trs) -- combined good-particle list assumed to exist
;    2004-07-08 (trs) -- micrographs are now four digits