; INTERSECTS DOC FILES BY DEFOCUS GROUP
;
; NOTE: Output doc files will have the format of the first input file(s), DF_TOTAL_LIST

; -------------------------- Parameter --------------------------
[progress-interval] = 4  ; progress message written to screen every Nth defocus group

; ---------------------------- Inputs ----------------------------
fr l
[io_dir]../Reconstruction2                                     ; input/output directory
fr l
[df_group_list]../Reconstruction/sel_group                     ; defocus-group doc file
;        DF_GROUP     NUMPARTS    AVGDEFOCUS
;          used                     copied
fr l
[df_total_list]../Reconstruction/sel_particles_{***[grp-num]}  ; total-particle list
;     GROUP_SLICE
fr l
[df_subset_list][io_dir]/supsel_particles_{***[grp-num]}       ; subset list
;     GROUP_SLICE

; --------------------------- Outputs ---------------------------
fr l
[df_intersection][io_dir]/sel_particles_{***[grp-num]}         ; intersection list, for each defocus group
fr l
[df_difference][io_dir]/deselect_{***[grp-num]}                ; difference list, for each defocus group
fr l
[defgrps][io_dir]/sel_group-supclass                           ; defocus-group doc
;  DF_GROUP    #PARTICLES   AVGDEFOCUS
fr l
[defgrps_sorted][io_dir]/sel_group_sorted-supclass             ; sorted defocus-group doc
;  DF_GROUP    #PARTICLES   AVGDEFOCUS

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

fr l
[temp_intersect_unrenum]tmpdocand_unrenum
fr l
[temp_difference_unrenum]tmpdocsubtract
fr l
[temp_defgrps_unreversed]tmpsort_unreversed

de
[defgrps]
SD /     DF_GROUP    #PARTICLES   AVGDEFOCUS
[defgrps]
de
[defgrps_sorted]
SD /     DF_GROUP    #PARTICLES   AVGDEFOCUS
[defgrps_sorted]

vm
echo "Intersecting doc files" ; date ; echo

; initialize particle-counter
[good-counter] = 0

; get #groups
ud n [num-grps]
[df_group_list]

; loop through groups
do [grp-key] = 1,[num-grps]
    ; get current defocus-group number, defocus
    ud ic [grp-key], [grp-num],x72,[avg-defocus]
    [df_group_list]

    if (int([grp-num]/[progress-interval]).eq.[grp-num]/[progress-interval]) then
        vm
        echo "Working on group #{***[grp-num]}, {***[grp-key]}th group out of {***[num-grps]}"
    endif

    ; intersect particle lists
    doc and
    [df_total_list]
    [df_subset_list]
    [temp_intersect_unrenum]
    (1)  ; column# to intersect: df-slice#

    doc ren
    [temp_intersect_unrenum]
    [df_intersection]

    ; get #particles
    ud n [num-parts]
    [df_intersection]

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

    SD /      DF_SLICE     MICSLICE     DF_GROUP    MICROGRAPH   GLOBAL_PART 
    [df_intersection]
    sd e
    [df_intersection]

    ; subtract particle lists
    doc subtract
    [df_total_list]
    [df_subset_list]
    [temp_difference_unrenum]
    (1)  ; column# to subtract: df-slice#

    ; renumber difference doc
    doc ren
    [temp_difference_unrenum]
    [df_difference]

    SD /      DF_SLICE     MICSLICE     DF_GROUP    MICROGRAPH   GLOBAL_PART 
    [df_difference]
    sd e
    [df_difference]

    sd [grp-key], [grp-num],[num-parts],[avg-defocus]
    [defgrps]
enddo
; end group-loop

; clean up
[dummy] = -[num-grps]
SD /     TOTALPARTS
[defgrps]
sd [dummy], [good-counter]
[defgrps]
ud ice
[df_group_list]
sd e
[defgrps]
de
[temp_intersect_unrenum]
de
[temp_difference_unrenum]


; SORT SEL_GROUP BY #PARTICLES

; sort by #particles
doc sort
[defgrps]
[temp_defgrps_unreversed]
(2)  ; column# to sort: #particles
Y    ; renumber?

; loop though defocus-groups (max: x76)
do lb6 [grp-key]=1,[num-grps]
    ; count from end
    [grp-num] = [num-grps] - [grp-key] + 1

    ; read group#, #particles (x52), defocus (x53)
    ud ic,[grp-key],[grp-num],x52,x53
    [temp_defgrps_unreversed]

    ; write to sorted doc
    sd [grp-key],[grp-num],x52,x53
    [defgrps_sorted]
lb6
; end group-loop

; clean up
ud ice
[temp_defgrps_unreversed]
de
[temp_defgrps_unreversed]
sd e
[defgrps_sorted]

vm
echo ; echo "Done -- Found {******[good-counter]} particles" ; date

en d

; Modified 2011-01-12