; GENERATE MATCHED FILTER
; 
; FSC-masking adapted from JSL's makegauss.bat

; -------------------- Parameter --------------------

[radius] = -1  ; object radius for masking before FSC, pixels (use <0 to determine from PARAMS)

; --------------------- Inputs ---------------------
fr l
[parameter_doc]../params                           ; parameter file
fr l
[recon_dir]../Reconstruction                       ; output reconstruction directory
fr l
[odd_half_volume][recon_dir]/vol001_odd            ; first half-set volume
fr l
[even_half_volume][recon_dir]/vol001_even          ; second half-set volume

; --------------------- Output ---------------------
fr l
[matched_filter_doc][recon_dir]/docmatched_vol001  ; output matched-filter doc

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

vm
echo "Generating matched-filter doc" ; date

fr l
[fsc_doc]tmpfscdoc

; get volume dimension
ud 17,[idim]
[parameter_doc]

; calculate center
[center] = [idim]/2 + 1

; calculate radius, if necessary
if([radius].le.0) then
    ; get diameter from PARAMS
    ud 18,[part-diam]
    [parameter_doc]

    [radius] = [part-diam]/2
endif

ud e  ; close doc

; create Gaussian
mo 3
_11
[idim],[idim],[idim]        ; dimensions
G                           ; _G_aussian
[center],[center],[center]  ; center coordinates
[radius],[radius],[radius]  ; Gaussian falloff

; get statistics
fs [max]
_11

; lift maximum to 1
ar
_11
_12
p1/[max]

; multiply volumes by mask
mu
[odd_half_volume]
_12  ; INPUT: mask
_21  ; OUTPUT
*

mu
[even_half_volume]
_12  ; INPUT: mask
_22  ; OUTPUT
*

rf 3 [res-pix],[res-freq]
_21        ; INPUT: odd_half_volume
_22        ; INPUT: even_half_volume
(1)        ; ring width (NEEDS TO BE 1 unless volume padded)
(0.8,1.2)  ; scale-factor range
C          ; missing _C_one
(90)       ; maximum tilt angle
(3)        ; factor for noise comparison
[fsc_doc]

[res-pix]
[res-freq]

vm
echo "Nominal resolution at 0.5FSC: {%f6.4%[res-freq]} pixels^-1"

; get #lines from resolution doc
ud n, [num-fsc-lines]
[fsc_doc]

de  ; clean up pre-existing file
[matched_filter_doc]

; loop through Radii
do lb1 [fsc-line]=3,[num-fsc-lines]
    ; get FSC (third column)
    ud ic [fsc-line], [spat-freq], [dummy], [fsc-value]
    [fsc_doc]

    ; write FSC to new document
    sd [fsc-line], [fsc-value], [spat-freq]
    [matched_filter_doc]
lb1
; end Radius-loop

; clean up
ud ice
[fsc_doc]
de
[fsc_doc]
sd e
[matched_filter_doc]

en  ; saving results file to refer back to nominal resolution

; Modified 2009-05-29
;    2008-01-15 (trs) -- now stand-alone batch file