; Apply low pass filter to set of particle image stacks
;
; PURPOSE: Apply low pass filter to set of particle image stacks.
;
; SOURCE: spider/docs/techs/recon1/Procs/denoise-imgs.spi
;
; USAGE: clean ; spider spi/dat @denoise-imgs
;
; ------------ Parameters ----------------------------------------
[filter-type] = 7 ; Filter type: Butterworth low-pass
; Reasonable ranges for Butterworth parameters:
; (0.05,0.3) for high defocus; (0.02,0.15) for low defocus
[par1] = 0.05 ; Filter parameter 1 = passband for Butterworth,
; filter radius for all others)
[par2] = 0.3 ; Filter parameter 2 = stopband for Butterworth,
; temperature for Fermi, ignored for all others)
; ----------- Input files --------------
[sel_micrograph] = '../sel_micrograph' ; Micrograph selection file (one)
[ser] = 'win/data_bymic_****' ; Unfiltered particle image stacks (one/micrograph)
; ----------- Output files --------------
[filtdir] = 'filt' ; Directory for filtered output images
[out] = '[filtdir]/data_bymic_****' ; Filtered particle image stacks (one/micrograph)
; -------------- END BATCH HEADER -------------
MD ; Use all available processors
SET MP
0
MD ; Skip unnecessary output
VB OFF
SYS ; Make directory for output
mkdir -p [filtdir]
SYS
echo ' 'Applying Low pass filter to images from micrograph stacks ; echo
DO ; Loop over all micrographs ----------------
UD NEXT [key],[mic] ; Get the micrograph number
[sel_micrograph] ; Micrograph selection file (input)
IF ( [key] <= 0 ) EXIT
FI H [maxim] ; Get number of particles in micrograph
[ser]@[mic] ; Raw images stack (input)
MAXIM ; Header location for # of images in file
DO [part] = 1,[maxim] ; Loop over all particle numbers -----------
IF ( [filter-type] >= 5 ) THEN
FQ
[ser]@******[mic][part] ; Raw images file (input)
[out]@******[mic][part] ; Filtered images file (output)
[filter-type] ; Filter type = Butterworth, Fermi
[par1],[par2] ; Passband, stopband
ELSE
FQ
[ser]@******[mic][part] ; Raw images file (input)
[out]@******[mic][part] ; Filtered images file (output)
[filter-type] ; Filter type = top hat, Gaussian
[par1] ; Filter radius
ENDIF
ENDDO ; End Loop over all particle numbers --------
SYS
echo ' 'Filtered: {%I6%[maxim]} images from micrograph: {%I4%[mic]}
ENDDO ; End loop over all micrographs -------------
UD NEXT END ; End doc file use
[sel_micrograph]
SYS
echo
EN
;