Add tutorial data of CTF Correction

	new file:   CTFCorrection/CTFCorrection1/Makefile
	new file:   CTFCorrection/CTFCorrection1/example.tif

diff --git a/CTFCorrection/CTFCorrection1/Makefile b/CTFCorrection/CTFCorrection1/Makefile
new file mode 100644 (file)
index 0000000..85d14f8
--- /dev/null
+++ b/CTFCorrection/CTFCorrection1/Makefile
@@ -0,0 +1,153 @@
+.SUFFIXES: .tif .mrc .cen .nor .fft .ctfinfoauto \
+           .ctfinfo .ctf .ctfps
+
+-include TIFS
+-include MRCS
+-include CENS
+-include NORS
+-include FFTS
+-include CTFAutoList
+-include CTFInfoList
+-include CTFS
+
+#
+# Setting Parameter
+# [A/pixel]
+RESOLUTION=3.80
+
+# JOB Number
+JN=-j 4
+
+#####################
+Help::
+       @echo "----- How To Use -----"
+       @echo "1. Prepare files(xxxx.tif) to be analyzed."
+       @echo "2. make TIF2CTF"
+       @echo ""
+       @echo "--- Special Target ---"
+       @echo "make DispCEN"
+       @echo "make DispCTF"
+       @echo "make PrintCTF"
+       @echo ""
+       @echo "--- Current Parameter ---"
+       @echo "RESOLUTION: $(RESOLUTION) [A/pixel]"
+       @echo "Job number for make: $(JN)" 
+
+mrc:          $(TIFS:.tif=.mrc)
+cen:          $(MRCS:.mrc=.cen)
+nor:          $(CENS:.cen=.nor)
+fft:          $(NORS:.nor=.fft)
+ctfinfoauto:  $(FFTS:.fft=.ctfinfoauto)
+ctfinfo:      $(CTFAutoList:.ctfinfoauto=.ctfinfo)
+ctf:          $(CTFInfoList:.ctfinfo=.ctf)
+ctfps:        $(CTFInfoList:.ctfinfo=.ctfps)
+
+TIF2CTF::
+       make TIFS; make $(JN) mrc;
+       make MRCS; make $(JN) cen;
+       make CENS; make $(JN) nor;
+       make NORS; make $(JN) fft;
+       make FFTS; make $(JN) ctfinfoauto;
+       make CTFAutoList; make ctfinfo;
+       make CTFInfoList; make $(JN) ctf;
+       make CTFS
+
+TIFS::
+       echo "TIFS=\\" > TIFS
+       ls -1 *.tif | sed s/tif/tif\\\\/ >> TIFS
+       echo "" >> TIFS
+
+MRCS::
+       echo "MRCS=\\" > MRCS
+       ls -1 *.mrc | sed s/mrc/mrc\\\\/ >> MRCS
+       echo "" >> MRCS
+
+CENS::
+       echo "CENS=\\" > CENS
+       ls -1 *.cen | sed s/cen/cen\\\\/ >> CENS
+       echo "" >> CENS 
+
+NORS::
+       echo "NORS=\\" > NORS
+       ls -1 *.nor | sed s/nor/nor\\\\/ >> NORS
+       echo "" >> NORS
+
+FFTS::
+       echo "FFTS=\\" > FFTS
+       ls -1 *.fft | sed s/fft/fft\\\\/ >> FFTS
+       echo "" >> FFTS
+
+CTFAutoList::
+       echo "CTFAutoList=\\" > CTFAutoList
+       ls -1 *.ctfinfoauto | sed s/ctfinfoauto/ctfinfoauto\\\\/ >> CTFAutoList
+       echo "" >> CTFAutoList
+
+CTFInfoList::
+       echo "CTFInfoList=\\" > CTFInfoList
+       ls -1 *.ctfinfo | sed s/ctfinfo/ctfinfo\\\\/ >> CTFInfoList
+       echo "" >> CTFInfoList
+
+CTFS::
+       echo "CTFS=\\" > CTFS
+       ls -1 *.ctf | sed s/ctf/ctf\\\\/ >> CTFS
+       echo "" >> CTFS
+
+.tif.mrc:
+       tiff2mrc -i $*.tif -o $*.mrc -r $(RESOLUTION) -m 0
+
+.mrc.cen:
+       mrcImageCenterGet -i $*.mrc -o $*.cen -Nx 1000 -Ny 1000
+
+DispCEN:
+       for i in $(CENS) ;\
+       do \
+               echo $$i;\
+               Display2 -i $$i;\
+       done
+
+.cen.nor:
+       mrcImageAbnormalValueRemove -i $*.cen -o $*.nor -u 65535 16384 -m 1
+
+.nor.fft:
+       mrcImageFFT -i $*.nor -o $*.fft
+
+.fft.ctfinfoauto:
+       ctfDetermine -i $*.fft -o $*.ctfinfoauto -D 50000 -m 128 \
+                                -CutLow 0.025 -CutHigh 0.15 -d 3 -Cc 0.7 -Cs 2.1
+
+.ctfinfoauto.ctfinfo:
+       if [ ! -f $*.ctfinfo ] ; then \
+               if [ -f default.ctfinfo ] ; then \
+                       cat default.ctfinfo >> $*.ctfinfo ; \
+               else \
+                       cat $*.ctfinfoauto >> $*.ctfinfo ; \
+               fi \
+       fi
+       ctfDisplay -i $*.fft
+       mv $@ $@.tmp
+       grep .: $@.tmp > $@
+       awk '!/.ctfinfo/ {print $$0}' $@ > default.ctfinfo
+
+.ctfinfo.ctf:
+       mv $*.ctfinfo $*.ctfinfo.tmp2
+       grep .: $*.ctfinfo.tmp2 > $*.ctfinfo
+       mrcImageCTFCompensation -i $*.fft -info2 $*.ctfinfo -o $*.ctf -m 1
+
+.ctf.ctfps:
+       mrcImagePrint -i $*.ctf -o $*.ctfps  -I -A  -m 17 -S 0.08
+
+DispCTF:
+       for i in $(CTFS) ;\
+       do \
+               echo $$i;\
+               Display2 -i $$i -Inverse;\
+       done
+
+PrintCTF:
+       for i in $(CTFS) ;\
+       do \
+               echo $$i;\
+               if [ -f $$i ] ; then \
+                       make `basename $$i .ctf`.ctfps; \
+               fi \
+       done
\ No newline at end of file

diff --git a/CTFCorrection/CTFCorrection1/example.tif b/CTFCorrection/CTFCorrection1/example.tif
new file mode 100644 (file)
index 0000000..21b00b8
Binary files /dev/null and b/CTFCorrection/CTFCorrection1/example.tif differ