([mic],[zflag],[fflag],[deci],[nsam],[nrow],[keepspi])
; Converts a scanned file to SPIDER format
;
; PURPOSE: Converts a scanned file to SPIDER format (usually incore).
;
; SOURCE: spider/docs/techs/recon/newprogs/loadmic.spi
;
; RECEIVED: [deci] = Decimation factor
; [zflag] = Zip flag (0:Unzipped, 1:Zipped)
; [fflag] = Format (0:SPIDER, 1:HISCAN TIF, 2:PERKINELMER, 3:ZI SCANNER)
; [nsam] = HiScan X dimension
; [nrow] = HiScan Y dimension
; [keepspi] = Keep SPIDER decompressed file
;
; ----------- Input files --------------
FR ; Read from caller
?Micrograph template?[micgr] ; Usually: ../Micrographs/raw{****[mic]}
; ----------- Output files --------------
FR ; Read from caller, file usually incore!
?spider output file?[out] ; SPIDER file (output)
; ----------- Temp file for Nikon & Hiscan only --------------
FR ; Read from caller, file usually incore!
[?Temp scratch file?[temp] ; SPIDER file (output)
; -------------- END BATCH HEADER --------------------------
MD
TR OFF ; Loop info turned off
MD
VB OFF ; File info turned off
MD
() OFF ; No need for () in DO loops
; ----------- Check if files are gzip compressed ----------------
IF ([fflag].GT.0) THEN ; TIF input file
IQ FI [exists] ; See if TIF file exists
[micgr].tif
IF ([exists].EQ.0) THEN ; TIF file does not exist
IQ FI [exists] ; See if gzip'd TIF file exists
[micgr].tif.gz
IF ([exists].EQ.1) THEN ; Have a gzip's TIF file
VM ; Unzip the file (input)
gunzip -c [micgr].tif.gz > [micgr].tif
VM
echo " Unzipped: [micgr].tif.gz"
ENDIF
ENDIF
ELSE ; Not a TIF input
IQ FI [exists] ; See if SPIDER file exists
[micgr]
IF ([exists].EQ.0) THEN ; SPIDER file does not exist
IQ FI [exists] ; See if gzip'd SPIDER file exists
[micgr].$DATEXT.gz
IF ([exists].EQ.1) THEN ; Have a gzip'ed SPIDER file
VM ; Unzip the file (input)
gunzip -c [micgr].$DATEXT.gz > [micgr].$DATEXT
VM
echo " Unzipped: [micgr].$DATEXT.gz"
ENDIF
ENDIF
ENDIF
; --------- Conversion based on scanner type ------------------
IF ([fflag] .EQ. 0) THEN ; Already is a Spider file --------------- SPIDER
IF ([deci].GT.1) THEN ; Reduce size of file
DC S ; Decimate by summing neighboring pixels
[micgr] ; Spider file (input)
[out] ; Spider file (output)
[deci],[deci] ; Decimation factor
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NSAM,NROW
VM
echo " Decimated {*[deci]}X: [micgr].$DATEXT To: [out] -- {*****[x]} x {*****[y]} "
123456789 123456789 123456789 123456789
ELSE
CP ; May want to move to incore file
[micgr] ; Spider file (input)
[out] ; Spider file (output)
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NSAM,NROW
VM
echo " Copied: [micgr].$DATEXT To: [out] -- {*****[x]} x {*****[y]}"
123456789 123456789 123456789 123456789
ENDIF
ELSEIF ([fflag] .EQ. 1) THEN
CP FROM RAW ; Hiscan micrograph -------------------- HISCAN
[micgr].tif ; Hiscan file (input)
16 ; Bits / pixel
[raw] ; File (input)
[nsam],[nrow] ; Size
342 ; Header bytes
1 ; Most significant byte (1 / 2)
N ; Fold negatives?
[temp] ; Spider file (output)
AR ; Scale file
[temp] ; Spider file (input)
[out] ; Spider file (output)
log(p1+1) ; Scaling
IF ([deci].GT.1) THEN ; Reduction
DC S ; Decimate image - Sum neighbours
[out] ; Spider file (input)
[temp] ; Spider file (output)
[deci],[deci] ; Decimation factor
VM
echo " Decimated {*[deci]}X: [micgr].tif By: {*[deci]}X To: [out]"
CP ; Copy file
[temp] ; Spider file (input)
[out] ; Spider file (output)
VM
echo " Converted Hiscan: [micgr].tif To: [out]"
ENDIF
ELSEIF ([fflag] .EQ. 3) THEN
VM ; ZI tif file. Overview always = 1 ---------- ZI
zi2spi [micgr].tif [micgr].$DATEXT 1
IF ([deci].GT.1) THEN ; Reduction
DC S ; Decimate - Sum neighbouring pixels
[micgr] ; Spider file (input)
[out] ; Spider file (output)
[deci],[deci] ; Decimation factor
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NSAM,NROW
VM
echo " Decimated {*[deci]}X ZI: [micgr].tif To: [out] -- {*****[x]} x {*****[y]}"
ELSE
CP ; Copy Spider temp file
[micgr] ; Micrograph (input)
[out] ; Spider file (output)
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NSAM,NROW
VM
echo " Converted ZI: [micgr].tif To: [out] -- {*****[x]} x {*****[y]}"
ENDIF
DE ; Delete the Spider temp file
jnk-[micgr] ; (removed)
ELSEIF ([fflag].EQ.4) THEN
IF ([deci].GT.1) THEN ; Reduction
CP FROM NIKON ; Nikon Tif Scanner file ----------------- NIKON
[micgr].tif ; Nikon tif file (input)
[temp] ; Spider file (output)
DC S ; Decimate - sum neighboring pixels
[temp] ; Spider file (input)
[out] ; Spider file (output)
[deci],[deci] ; Decimation factor
VM
echo " Decimated {*[deci]}X Nikon: [micgr].tif To: [out]"
ELSE
CP FROM NIKON ; Nikon Tif Scanner file
[micgr].tif ; Nikon tif file (input)
[out] ; Spider file (output)
VM
echo " Converted Nikon: [micgr].tif To: [out]"
ENDIF
ENDIF
en
RE
; ----------- Undo zip source if necessary -----------( REMOVED, RISKY)
IF ([zflag]*[fflag] .GT. 0) THEN ; Both tif & zip flags set
DE ; Remove the .tif file
[micgr].tif ; File (removed)
VM
echo " Re-moved: [micgr].tif"
ELSEIF ([zflag].eq.1) THEN ; Only zip flag
IF ([keepspi].LE.0) THEN
DE ; Remove the de-zipped Spider file
[micgr] ; File (removed)
VM
echo " Re-moved: [micgr].$DATEXT"
ENDIF
ENDIF
RE
;