; Adapted from PFILT.BAT 
; apply low pass filter to and shrinks a set of particle images

; ------------------ Parameters ------------------
x11 = 7     ; filter type (7==Butterworth)
x21 = 37.6  ; filter parameter 1, Angstroms (pass-band if Butterworth, else filter radius)
x22 = 28.2  ; filter parameter 2, Angstroms (stop-band if Butterworth
            ; stop band for Butterworth, temperature for Fermi, else not required
x26 = 2     ; reduction/decimation factor (integer)

; -------------------- Inputs --------------------
fr l
[params]../params                                        ; parameter document
fr l
[df_group_list]sel_group                                 ; list of defocus groups
fr l
[slice2particle_lut]../Alignment/sel_particles_{***x77}  ; slice-to-particle lookup-table, for each group
;[slice2particle_lut]df{***x77}/select/particle_lut_083   ; slice-to-particle lookup-table, for one view
fr l
[alignment_doc]../Alignment/align_01_***                 ; AP SH doc template
fr l
[aligned_images]../Alignment/dala01_{***x77}@*****       ; aligned-image stack file-template

; -------------------- Output --------------------
fr l
[filtered]../Particles/flt/flt******             ; filtered-image prefix (unstacked)

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

vm
echo "Filtering images"; date

; get pixel size (x15)
ud 5,x15
[params]
ud e

; change filter radii to reciprocal pixels
x21 = x15/x21  ; pass-band
x22 = x15/x22  ; stop-band
; x15==pixel-size

; get #defocus-groups (x75)
ud n,x75
[df_group_list]

md
set mp
0

; loop through defocus-groups
DO LB7 x71=1,x75
    ; get defocus-group# (x77)
    ud ic,x71,x77
    [df_group_list]

    vm
    echo "On defocus-group #{***x77}, {***x71} out of {***x75}"

    ; get #particles (x50)
    ud n,x50
    [slice2particle_lut]

    ; loop through particles
    do lb1 x44=1,x50
        ; get particle# (x55)
        ud ic,x44,x55
        [slice2particle_lut]

        cp
        [aligned_images]x44
        _5
        ; x44==slice# in stack

        ; if Butterworth filter
        IF (x11.eq.7) THEN
            FQ np
            _5       ; input file
            _4       ; output file
            x11      ; filter type
            x21,x22  ; passband, stopband
        endif

        ; if Fermi filter
        IF (x11.eq.5) THEN
            FQ np
            _5       ; input file
            _4       ; output file
            x11      ; filter type = Fermi
            x21      ; filter radius
            x22      ; temperature cutoff
        endif

        ; if Gaussian or top-hat filter
        IF (x11.le.3) THEN
            FQ np
            _5       ; input file
            _4       ; output file
            x11      ; filter type = top hat, Gaussian
            x21      ; filter radius
        ENDIF

        ; check Euler-angle theta (x32) for mirroring
        ud ic,x44,x31,x32
        [alignment_doc]x77

        ; shrink and, if necessary, mirror
        if(x32.ge.180) then
            dc s
            _4
            _1
            x26,x26  ; reduction factor in x,y

            mr
            _1
            [filtered]x55
            y  ; mirror around y-axis
            ; x55==particle# (vs. slice# x44)
        else
            dc s
            _4
            [filtered]x55
            x26,x26  ; reduction factor in x,y
        endif
    lb1

    ; end particle-loop

    ; close in-core files
    ud ice
    [alignment_doc]x77
    ud ice
    [slice2particle_lut]
LB7  
; end group-loop

ud ice
[df_group_list]

vm
echo "Done"; date

EN D

; Modified 2007-05-30
;    2007-05-30 (trs & gsa) -- reflects change to input file sel_particles
;    2007-03-27 (trs & xa) -- reflects changes to input file sel_particles
;    2007-02-22 (trs & djt) -- bug fix for filenames
;    2007-01-24 (trs) -- input aligned images are now stacked
;    2006-08-17 (trs) -- bug fix for mirroring in prj001 
;    2006-04-05 (trs) -- changed units for filter radii
;    2004-12-28 (trs) -- mirrors aligned image, if necessary
;    2004-06-16 (trs) -- dusts images