; Calculates avg power spectra for a set of micrographs
;
; PURPOSE: ; Calculates avg 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] = 1 ; 1 = mask out center of spectrum; 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 LB1 [key]=1,[nummics] ; Loop over all micrographs -------------------
UD [key], [mic]
[sel_mic] ; Doc file (inpu)
VM
echo ' 'Processing micrograph: {*****[mic]}
; Get zip and format flags from parameter file
UD 1,[zflag] ; Get zip flag
[params]
UD 2,[fflag] ; Get tif flag
[params]
IF ([zflag]*[fflag].GT.0) THEN ; Both tif & zip flags set
VM ; Unzip the file
gunzip [micgr].tif.gz
GOTO LB3
ENDIF
IF ([zflag].GT.0) THEN ; Zip, but not tif, flag set
VM ; Unzip the file
gunzip [micgr].$DATEXT.gz
GOTO LB3
ENDIF
LB3
IF ([fflag].EQ.1) THEN
UD 3,x51 ; If it's a HiScan tif, get X,Y size parameters
[params]
UD 4,x52
[params]
CP FROM RAW
[micgr].tif ; Raw file (input)
(16) ; Bits per pixel
x51,x52 ; Columns & rows
(342) ; Header bytes
(1) ; Most significant byte
N ; Do not fold negatives
junk12987 ; Spider file (output)
AR
junk12987
_1
log(p1+1)
DE
junk12987
ENDIF
; If it's a ZI tif, make system call to zi2spi.
; NB OVERVIEW SHOULD ALWAYS = 1, USE 'DC S' TO REDUCE SIZE
IF ([fflag].EQ.3) THEN
VM ; Convert to SPIDER format
zi2spi [micgr].tif [micgr].$DATEXT 1
CP ; Place in incore file
[micgr]
_1
DE ; Delete the SPIDER format file
[micgr] ;
ENDIF
IF ([fflag].eq.0) THEN ; If not tif, still need to put input in _1
CP ; Place in incore file
[micgr] ; (input)
_1
ENDIF
; Size reduction, if any
IF ([deci].EQ.1) GOTO LB7 ; No reduction
IF ([deci].LT.1) THEN
UD 16,[deci] ; Get reduction factor from param file
[params] ; (input)
IF ([deci].LE.1) GOTO LB7
ENDIF
DC S ; Decimate image - Sum neighbouring pixels
_1
_2
[deci],[deci] ; Decimation factor
CP ; Copy file
_2
_1
LB7
; If the output doc files already exist, delete them
DE
[roo]
@power_p1([winsiz],[xover],[yover],[xd],[yd],[mask])
_1
[spectrum]
[roo]
[tmparr]
IF ([zflag]*[fflag].GT.0) THEN ; Both tif & zip flags set
VM
gzip [micgr].tif
GOTO LB4
ENDIF
IF ([zflag].eq.1) THEN ; Only zip flag
VM
gzip [micgr].$DATEXT
GOTO LB4
ENDIF
LB4
LB1
EN
;