; Calculates avg power spectra for a set of micrographs
;
; PURPOSE: ; Calculates average power spectra for a set of micrographs.
; Converts a scanned file to SPIDER format.
; Input: window size, percentage of the overlap
; distance of the window from the micrograph border
; Spectra placed in: power/roo***
;
; SOURCE: power.spi
;
; CALLS: power_p1.spi
;
; Edit the following parameters as needed, including the filenames
[winsiz] = 500 ; Window size of small pieces (Sx=Sy)
[xover] = 50 ; % of the overlap in x
[yover] = 50 ; % of the overlap in y
[xd] = 500 ; Dist. from the edge (x)
[yd] = 500 ; Dist. from the edge (y)
[mask] = 225 ; Power spectrum mask radius (Angstroms); 0 = don't mask
; [deci] = decimation factor for 'DC S' operation
; 0 = get value from param file (key=16)
; 1 = full sized image
; 2 = 1/2 size
; 4 = 1/4 size
[deci] = 1 ; Decimation factor (0 = get value from param file)
; ----------- Input files --------------
FR L
[params]../params ; Parameter file
FR L
[sel_mic]../sel_micrograph ; Micrograph selection doc file
FR L
[micgr]../Micrographs/mic{****[mic]} ; Micrographs
; ----------- Output files --------------
FR L
[outdir]power ; Power spectra output directory
FR L
[spectrum][outdir]/pw_avg{****[mic]} ; Power spectra
FR L
[roo][outdir]/roo{****[mic]} ; Rotational average (doc file)
; -------------- END BATCH HEADER --------------------------
; This gets the file numbers,
; checks if they need to be unzipped or converted,
; then calls power_p1 in the main loop
UD N [nummics] ; Get number of micrographs
[sel_mic]
VM ; Make sure output dir. present
mkdir -p [outdir]
FR G ; Name for incore doc file
[tmparr]tmparray
[winsizd2]=[winsiz]/2
SD IC NEW ; Create an in-core doc file array
[tmparr]
4,[winsizd2] ; Creates a 4 column doc file
DO [key]=1,[nummics] ; Loop over all micrographs -------------------
UD [key], [mic]
[sel_mic] ; Doc file (input)
VM
echo ' 'Processing micrograph: {*****[mic]}
; ----- Get zip & format flags from parameter file (can params vary??) ---------
UD 1,[zflag] ; Get zip flag
[params]
UD 2,[fflag] ; Get tif flag
[params]
; ----------- Checks if files are gzip compressed ------------------
IF ([zflag]*[fflag].GT.0) THEN ; Both tif & zip flags set
VM ; Unzip the file
gunzip [micgr].tif.gz
ELSEIF ([zflag].GT.0) THEN ; Zip, but not tif, flag set
VM ; Unzip the file
gunzip [micgr].$DATEXT.gz
ENDIF
; ----------- Conversion based on scanner type -------------------
IF ([fflag] .eq .0) THEN ; Spider file, need to put input in _1
CP ; Place in incore file
[micgr] ; Spider file (input)
_1 ; Spider file (output)
ELSEIF ([fflag] .EQ. 1) THEN
UD 3,[nsam] ; HiScan raw file, Get X,Y size parameters
[params] ; Params file (input)
UD 4,[nrow] ;
[params] ; Params file (input)
CP FROM RAW
16 ; Bits / pixel
[micgr].tif ; Raw file (input)
[raw] ; File (input)
[nsam],[nrow] ; Size
(342) ; Header bytes
(1)
N
_2 ; Spider file (output)
AR
_2 ; Spider file (input)
_1 ; Spider file (output)
log(p1+1)
ELSEIF ([fflag] .EQ. 3) THEN
VM ; ZI tif file. Overview should always = 1
zi2spi [micgr].tif [micgr].$DATEXT 1
CP ; Place in incore file
[micgr]
_1 ; Spider file (output)
DE ; Delete the SPIDER format file
[micgr] ;
ELSEIF ([format].EQ.4) THEN
CP FROM NIKON ; Nikon Tif Scanner file
[micgr].tif ; Nikon tif file (input)
_1 ; Spider file (output)
ENDIF
; ----------- Size reduction, if any -------------------
IF ([deci].LT.1) THEN
UD 16,[deci] ; Get reduction factor from param file
[params] ; Param file (input)
ENDIF
IF ([deci].GT.1) THEN ; Reduction
DC S ; Decimate image - Sum neighbouring pixels
_1 ; Spider file (input)
_2 ; Spider file (output)
[deci],[deci] ; Decimation factor
CP ; Copy file
_2 ; Spider file (input)
_1 ; Spider file (output)
ENDIF
; ----------- Masking ---------------------------------------
IF ([mask].NE.0) THEN
UD 5,[pxsiz] ; Get pixel size
[params] ; Params file (input)
[pxsiz]=[pxsiz]*[deci] ; Adjust pixel size for decimation
[radius]=2*[pxsiz]/[mask] ; Mask radius (now in 1/px)
ENDIF
; If the output doc files already exist, delete them
DE
[roo]
@power_p1([winsiz],[xover],[yover],[xd],[yd],[radius])
_1
[spectrum]
[roo]
[tmparr]
; ----------- Rezip if necessary -------------------
IF ([zflag]*[fflag] .GT. 0) THEN ; Both tif & zip flags set
VM ; Recompress the file
gzip [micgr].tif
ELSEIF ([zflag].eq.1) THEN ; Only zip flag
VM ; Recompress the file
gzip [micgr].$DATEXT
ENDIF
ENDDO
EN
;