; CREATES APMQ FILES FROM APSH FILES BY DEFOCUS GROUP

; -------- Parameter --------
x56 = 3  ; print progress message to screen every (x56)th micrograph

; ---------- Inputs ----------
fr g
[neg_list]../filenums                   ; micrograph list
fr g
[neg_particle_table]../Particles/order  ; micrograph-to-particle look-up table
fr g
[apsh_doc]align01_                      ; APSH filename template, for each micrograph

; --------- Outputs ---------
fr g
[neg_apmq_doc]apmq/apmq     ; AMPQ filename template, for each micrograph
fr g
[combined_apmq_doc]docapmq  ; combined APMQ doc

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

; get number of micrographs
ud n,x76
[neg_particle_table]

vm
echo "Creating APMQ files"; date

; loop through micrographs
do lb7 x71=1,x76
    ; get micrograph# (x70), first (x64), last (x65) particles
    ud ic,x71,x70,x62,x63,x64,x65
    [neg_particle_table]

    ; print progress message
    if (int(x71/x56).eq.x71/x56) then
        vm
        echo "Working on micrograph# {****x70}, {***x71} out of {***x76}"
    endif

    ; prepare output APMQ files
    de
    [neg_apmq_doc]{****x70}
    SD /     REF_PROJ       CCC        ROT.ANGLE    X-SHIFT      Y-SHIFT     PARTICLE#
    [neg_apmq_doc]{****x70}

    ; loop through particles
    do lb6 x60=x64,x65
        ; read APSH parameters
        ud ic,x60,x11,x12,x13,x14,x15,x16,x17,x18,x19,x20,x21,x22,x23,x24,x25
        [apsh_doc]{****x70}
        ; x14==ref-view#, x15=particle#, x16==in-plane rotation, x17==x-shift, x18==y-shift, x21=CCC

        x66=x60-x64+1  ; x66==particle-counter for current micrograph

        ; write APMQ parameters
        sd x66,x14,x21,x16,x17,x18,x15
        [neg_apmq_doc]{****x70}
        ; x14==ref-view#, x21=CCC, x16==in-plane rotation, x17==x-shift, x18==y-shift, x15=particle#

    lb6
    ; end particle-loop

    ud ice  ; close in-core, APSH file
    [apsh_doc]{****x70}
lb7
; end micrograph-loop

; combine APMQ files
vm
echo "Combining APMQ files"

doc combine
[neg_apmq_doc]****
[neg_list]
[combined_apmq_doc]

SD /     REF_PROJ       CCC        ROT.ANGLE    X-SHIFT      Y-SHIFT     PARTICLE#
[combined_apmq_doc]

ud ice  ; close in-core micrograph-list
[neg_particle_table]

vm
echo "Done"; date

en d

; Modified 2005-03-09
;    2004-11-30 (trs) -- Micrograph# is now the first column in order
;    2004-07-08 (trs) -- Assumes keys in order are consecutive (!=micrograph#)
; (This would probably run faster if it used SD IC. --T.R.S.)