; Estimates defocus values from power spectra
;
; PURPOSE: Estimates defocus from 2D power spectra.
; Uses SPIDER operation 'TF ED'
;
; SOURCE: defocus.spi
;
; CALLS: calcparms
;
; ----------- Input files --------------
FR G
[pow]power/pw_avg{****[mic]} ; 2D power spectra
FR G
[sel_mic]../sel_micrograph ; Micrograph file numbers
FR G
[params]../params ; Reconstruction parameter file
; ----------- Output files --------------
FR G
[ctf]power/ctf{***[mic]} ; Doc files with spectrum, envelope, noise
FR G
[out]defocus ; Doc file of defocus values for micrographs
; -------------- END BATCH HEADER --------------------------
MD ; Skip unnecessary output
VB OFF
MD ; Skip unnecessary output
TR OFF
DE ; Delete output doc file
[out]
SD / Micrograph Defocus Astig.Ang Astig.Mag Cutoff.Freq
[out]
; Make sure all parameters are calculated
@calcparms
[params]
UD 5,[pxsiz] ; Pixel size
[params]
UD 7,[spa] ; Spherical aberration
[params]
UD 12,[acr] ; Amplitude contrast ratio
[params]
UD 14,[lambda] ; Lambda
[params]
VM
echo ' 'Computing defocus values for selected micrographs
DO ; Loop over all micrographs -------------------
UD NEXT [key],[mic] ; Get micrograph number
[sel_mic] ; Doc file (input)
IF([key].LE.0) EXIT
DE ; Delete output doc file
[ctf]
; Transfer Function -- Estimation of CTF parameters
TF ED [v12],[v13],[v14],[v15],[v16]
[pow] ; 2D spectrum (input)
([pxsiz], [spa]) ; Pixel size (A), Spherical aberration (mm)
([lambda]) ; Lambda
([acr]) ; Ampl. contrast ratio
[ctf] ; Doc file (output)
; Save parameters for each group in doc file
SD [key], [mic],[v14],[v12],[v13],[v16]
[out] ; Doc file (output)
;VM
;echo ' '{%f8.2%[mic]},{%f8.2%[v14]},{%f8.2%[v12]},{%f8.2%[v13]},{%f8.2%[v16]}
ENDDO
UD NEXT E ; Finished
[sel_mic] ; Doc file
VM
echo ' '
EN