([mic],[zflag],[fflag],[deci],[nsam],[nrow],[keepspi])
; Converts a scanned file to SPIDER format
;
; SOURCE: spider/docs/techs/recon/newprogs/load-mic.spi
;
; PURPOSE: Converts a scanned file to SPIDER format (usually incore).
;
; 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
; ----------- Check if files are gzip compressed ----------------
IF ( [fflag] > 0 ) THEN ; TIF input file
IQ FI [exists] ; See if TIF file exists
[micgr].tif
IF ( [exists] == 0 ) THEN ; TIF file does not exist
IQ FI [exists] ; See if gzip'd TIF file exists
[micgr].tif.gz
IF ( [exists]== 1 ) THEN ; Have a gzip's TIF file
SYS ; Unzip the file (input)
gunzip -c [micgr].tif.gz > [micgr].tif
SYS
echo " Unzipped: [micgr].tif.gz"
ENDIF
ENDIF
ELSE ; Not a TIF input
IQ FI [exists] ; See if SPIDER file exists
[micgr]
IF ( [exists] == 0 ) THEN ; SPIDER file does not exist
IQ FI [exists] ; See if gzip'd SPIDER file exists
[micgr].$DATEXT.gz
IF ([exists]==1) THEN ; Have a gzip'ed SPIDER file
SYS ; Unzip the file (input)
gunzip -c [micgr].$DATEXT.gz > [micgr].$DATEXT
SYS
echo " Unzipped: [micgr].$DATEXT.gz"
ENDIF
ENDIF
ENDIF
; --------- Conversion based on scanner type ------------------
IF ( [fflag] == 0 ) THEN ; Already is a Spider file --------------- SPIDER
IF ( [deci] > 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)
NX,NY
SYS
echo " Decimated {*[deci]}X: [micgr].$DATEXT To: [out] -- {*****[x]} x {*****[y]} "
123456789 123456789 123456789 123456789
ELSE
CP ; May want to move to incore file
[micgr] ; Spider file (input)
[out] ; Spider file (output)
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NX,NY
SYS
echo " Copied: [micgr].$DATEXT To: [out] -- {*****[x]} x {*****[y]}"
123456789 123456789 123456789 123456789
ENDIF
ELSEIF ([fflag] == 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] > 1 ) THEN ; Reduction
DC S ; Decimate image - Sum neighbours
[out] ; Spider file (input)
[temp] ; Spider file (output)
[deci],[deci] ; Decimation factor
SYS
echo " Decimated {*[deci]}X: [micgr].tif By: {*[deci]}X To: [out]"
CP ; Copy file
[temp] ; Spider file (input)
[out] ; Spider file (output)
SYS
echo " Converted Hiscan: [micgr].tif To: [out]"
ENDIF
ELSEIF ([fflag] == 3) THEN
SYS ; ZI tif file. Overview always = 1 ---------- ZI
zi2spi [micgr].tif [micgr].$DATEXT 1
IF ([deci] > 1) THEN ; Reduction
DC S ; Decimate - Sum neighbouring pixels
[micgr] ; Spider file (input)
[out] ; Spider file (output)
[deci],[deci] ; Decimation factor
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NX, NY
SYS
echo " Decimated {*[deci]}X ZI: [micgr].tif To: [out] -- {*****[x]} x {*****[y]}"
ELSE
CP ; Copy Spider temp file
[micgr] ; Micrograph (input)
[out] ; Spider file (output)
FI H [x],[y] ; Get dimensions of converted image
[out] ; Micrograph image (input)
NX,NY
SYS
echo " Converted ZI: [micgr].tif To: [out] -- {*****[x]} x {*****[y]}"
ENDIF
DE ; Delete the Spider temp file
jnk-[micgr] ; (removed)
ELSEIF ([fflag]==4) THEN
IF ([deci] > 1 ) THEN ; Reduction
CP FROM NIKON ; Nikon Tif Scanner file ----------------- NIKON
[micgr].tif ; Nikon tif file (input)
[temp] ; Spider file (output)
DC S ; Decimate - sum neighboring pixels
[temp] ; Spider file (input)
[out] ; Spider file (output)
[deci],[deci] ; Decimation factor
SYS
echo " Decimated {*[deci]}X Nikon: [micgr].tif To: [out]"
ELSE
CP FROM NIKON ; Nikon Tif Scanner file
[micgr].tif ; Nikon tif file (input)
[out] ; Spider file (output)
SYS
echo " Converted Nikon: [micgr].tif To: [out]"
ENDIF
ELSEIF ( [fflag] == 5) THEN
; CP FROM MRC
; [raw]
; [spider]
; N,Y ; No byte flip, flip top+bottom
; ; (Doesn't work on all MRC files)
[temp_spi] = 'tmpspi-unflipped'
SYS
[xic] -i [micgr].mrc -o [temp_spi].$DATEXT
MR
[temp_spi]
[out]
Y ; Flip around _y_-axis
DE
[temp_spi]
SYS
echo " Converted MRC: [micgr].mrc To: [out]"
ELSE
SYS ;
echo " Unsupported input format: {***[format]}"
ENDIF
RE
; ----------- Undo zip source if necessary -----------( REMOVED, RISKY)
IF ( [zflag]*[fflag] > 0) THEN ; Both tif & zip flags set
DE ; Remove the .tif file
[micgr].tif ; File (removed)
SYS
echo " Re-moved: [micgr].tif"
ELSEIF ( [zflag]==1 ) THEN ; Only zip flag
IF ( [keepspi] <= 0 ) THEN
DE ; Remove the de-zipped Spider file
[micgr] ; File (removed)
SYS
echo " Removed: [micgr].$DATEXT"
ENDIF
ENDIF
RE
; Modified 2016-05-24
; 2016-01-22 (trs) -- flips XMIPP-converted MRC file
; 2016-01-20 (trs) -- using XMIPP to convert MRC to SPIDER
;