; PURPOSE:  Apply low pass filter to a set of particle images.
;
; SOURCE:   pfilt2.spi    
;
; PARAMETERS:
;   filter arg1  (passband for Butterworth,
;                 filter radius for all others)
;
;   filter arg2  (stopband for Butterworth,
;                 temperature for Fermi,
;                 ignored for all others)
;
; Reasonable ranges for Butterworth parameters:
; (0.05,0.3) for high defocus; (0.02,0.15) for low defocus

[filter-type] = 7     ; Filter type: Butterworth low-pass
[par1] = 0.05         ; Filter parameter 1 = passband
[par2] = 0.3          ; Filter parameter 2 = stopband

; ----------- Input files --------------

FR G
[sel_micrograph]../sel_micrograph ; Micrograph selection file

FR L
[ser]win/winser_{****[mic]}@      ; Picked article image stack

; ----------- Output files --------------

FR L
[flt]winser_{****[mic]}@         ; Filtered particle image stacks

FR G
[fltdir]flt                      ; Directory for output images

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

MD                              ; Use all available processors
SET MP
0 
MD                              ; Skip unnecessary output 
VB OFF

VM                              ; Make directory for output
mkdir -p [fltdir]

FR G                            ; Set output location
[out] [fltdir]/[flt]

UD N [nummics] ; Get the number of micrograph files
[sel_micrograph]

DO LB1 [key]=1,[nummics]       ; Loop over all micrographs ---------------------

   UD [key],[mic]              ; Get the micrograph number
   [sel_micrograph]

   FI X [maxim]                ; Get number of particles in micrograph
   [ser]                       ; Raw images stack               (input)
   (26)                        ; Header location for number of images in file 

   DO LB2 [part] = 1,[maxim]   ; Loop over all particle numbers

      IF ([filter-type].GE.5) THEN
         FQ
         [ser]{******[part]}   ; Raw images file              (input)
         [out]{******[part]}   ; Filtered images file         (output)
         [filter-type]         ; Filter type = Butterworth, Fermi
         ([par1],[par2])       ; Passband, stopband

      ELSE 
         FQ
         [ser]{******[part]}   ; Raw images file              (input)
         [out]{******[part]}   ; Filtered images file         (output)
         [filter-type]         ; Filter type = top hat, Gaussian
         [par1]                ; Filter radius
      ENDIF
   LB2
   VM
   echo ' 'Filtered  {*****[maxim]} images from micrograph: {*****[mic]}

LB1
VM
echo ' ' 

EN D