; GENERATE BAD-PARTICLE LIST
; IN GOODPARTICLES FORMAT

; ---------------------- Parameter ----------------------
x56 = 2  ; prints progress message every (x56)th defocus group

; ------------------------ Inputs ------------------------
fr l
[df_group_list]../Reconstruction/sel_group_cclim         ; defocus-group selection list
fr l
[stack2particle_lut]../Reconstruction/stack2particle***  ; stack-to-particle lookup table
;       PARTICLE    MICROGRAPH    MIC_SLICE    GROUP_SLICE
fr l
[alignment_doc]../Reconstruction/align_01_***                   ; alignment doc
fr l
[df_dir]../Reconstruction/df***                                 ; input-output defocus-group directory
fr l
[good_particle_list]goodparticles                        ; good-particle list, in DF_DIR
;     GROUP_SLICE   PARTICLE       CCROT

; ----------------------- Outputs -----------------------
fr l
[total_particle_list]totalparticles                      ; total-particle list, in DF_DIR
;     GROUP_SLICE   PARTICLE       CCROT
fr l
[bad_particle_list]badparticles                          ; bad-particle list, in DF_DIR

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

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

; loop through defocus-groups
do lb7 [group-key] = 1,[num-groups]
    ; get group#
    ud ic [group-key],[group-num]
    [df_group_list]
    
    if (int([group-key]/x56).eq.[group-key]/x56) then
        vm
        echo "Working on defocus group {***[group-num]}, #{***[group-key]} out of {***[num-groups]}"
    endif
    
    de
    [df_dir][group-num]/[total_particle_list]
    SD /   GROUP_SLICE   PARTICLE       CCROT
    [df_dir][group-num]/[total_particle_list]
    
    ; get #particles
    ud n [num-particles]
    [stack2particle_lut][group-num]
    
    ; loop through particles
    do lb5 [slice-num] = 1,[num-particles]
        ; get ccrot from alignment doc
        ud ic [slice-num],x91,x92,x93,x94,x95,x96,x97,x98,x99,x90,[ccrot]
        [alignment_doc][group-num]
        
        ; get particle#
        ud ic [slice-num],[particle-num]
        [stack2particle_lut][group-num]
        
        ; write to total-particle doc
        sd [slice-num],[slice-num],[particle-num],[ccrot]
        [df_dir][group-num]/[total_particle_list]
    lb5
    ; end particle-loop
    
    ; close docs
    ud ice
    [alignment_doc][group-num]
    ud ice
    [stack2particle_lut][group-num]
    sd e
    [df_dir][group-num]/[total_particle_list]
    
    ; generate bad-particle list
    doc subtract
    [df_dir][group-num]/[total_particle_list]
    [df_dir][group-num]/[good_particle_list]
    [df_dir][group-num]/[bad_particle_list]_unrenum  ; OUTPUT
    (1)  ; column# to subtract: slice#
    
    doc ren
    [df_dir][group-num]/[bad_particle_list]_unrenum
    [df_dir][group-num]/[bad_particle_list]  ; OUTPUT
    
    SD /   GROUP_SLICE   PARTICLE       CCROT
    [df_dir][group-num]/[bad_particle_list]
    sd e
    [df_dir][group-num]/[bad_particle_list]
    de
    [df_dir][group-num]/[bad_particle_list]_unrenum
lb7
; end group-loop

ud ice
[df_group_list]

en d