([deci])
; Converts a scanned file to a SPIDER format
; SOURCE: spider/docs/techs/recon1/Procs/convert-p.spi
; PURPOSE: Converts a scanned file to a SPIDER format.
;
; [deci] = decimation factor for 'DC S' command
; 0 = Get value from param file (key=16)
; 1 = Full sized image
; 2 = 1/2 size
; 4 = 1/4 size
FR
?Parameter file? [params]
FR
?Input micrograph? [raw]
FR
?SPIDER output file? [spider]
; ----- Get zip & format flags from parameter file -----------------
UD 1, [sp_zflag]
[params]
UD 2, [sp_fflag]
[params]
; ----------- Checks if files are gzip compressed -------------------
IF ( [sp_zflag]*[sp_fflag] > 0) THEN
SYS ; Both tif & zip flags set
gunzip [raw].gz
SYS
echo " Unzipped: [raw].gz"
ELSEIF ( [sp_zflag] > 0 ) THEN
SYS ; Zip, but not tif, flag set
echo " Unzipping file "
SYS
gunzip [raw].$DATEXT.gz
SYS
echo " Unzipped: [raw].$DATEXT.gz"
ENDIF
; ----------- Conversion based on scanner type -------------------
IF ( [sp_fflag] == 0 ) THEN
CP ; Already a SPIDER file, put in output file
[raw] ; File (input)
[spider] ; File (output)
SYS
echo " Copied SPIDER file: [raw] To: [spider]"
ELSEIF ( [sp_fflag] == 1 ) THEN
UD 3,[sp_nx] ; HiScan raw file, Get X,Y size parameters
[params] ; Params file (input)
UD 4,[sp_ny] ;
[params]
CP FROM RAW
16 ; Bits / pixel
[raw] ; File (input)
[sp_nx],[sp_ny] ; Size
342 ; Header bytes
1
N
_1 ; File (output)
AR
_1 ; File (input)
[spider] ; File (output)
P1*(-1)+5
SYS
echo " Converted Hiscan: [raw] To: [spider]"
ELSEIF ( [sp_fflag] == 3 ) THEN
SYS ; ZI tif file. Overview should always = 1
zi2spi [raw] [spider].$DATEXT 1
SYS
echo " Converted ZI file: [raw] To: [spider].$DATEXT"
ELSEIF ( [sp_fflag] == 4) THEN
CP FROM NIKON ; Nikon Tif Scanner file
[raw]
[spider]
SYS
echo " Converted Nikon TIF: [raw] To: [spider]"
ELSE
SYS ;
echo " Unsupported input format: {***[sp_fflag]}"
ENDIF
; ----------- Rezip if necessary -------------------
IF ( [sp_zflag]*[sp_fflag] > 0) THEN
SYS ; Both tif & zip flags set
gzip [raw]
SYS
echo " Re-zipped: [raw]"
ELSEIF ([sp_zflag] == 1) THEN ;
SYS ; Recompress the file
gzip [raw].$DATEXT
SYS
echo " Re-zipped: [raw].$DATEXT"
ENDIF
; ----------- Size reduction, if any -------------------
IF ( [deci] < 1) THEN
UD 16,[sp_deci] ; Get reduction factor from param file
[params] ; Param file (input)
[deci] = [sp_deci]
ENDIF
IF ( [deci] > 1) THEN ; Reduction
DC S ; Reduce size
[spider]
_1 ; File (input)
[deci],[deci] ; Reduction
CP ; Copy
_1 ; File (input)
[spider] ; File (output)
SYS
echo " Decimated: [raw] By: {**[deci]}"
ENDIF
RE
;