Xmipp2coord: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
(6 intermediate revisions by one other user not shown) | |||
Line 1: | Line 1: | ||
#!/usr/bin/env csh | |||
#!/usr/bin/env csh | # | ||
# | # | ||
# | if ($# == 3 ) then | ||
if ($# == 3 ) then | set xmdfile = $1 | ||
set tablename = $2 | |||
set downsample = $3 | |||
relion_star_printtable ${xmdfile} ${tablename} _micrograph _xcoor _ycoor | awk -F"/" '{print $NF}' | sort > tt.dat | |||
foreach mic (`cat tt.dat | awk '{print $1}' | uniq`) | |||
set coordfile=`echo ${mic} | sed 's|.mrc|.coord|'` | |||
echo "Creating " $coordfile " ... " | |||
echo " x y density" > ${coordfile} | |||
grep ${mic} tt.dat | awk -v"down=${downsample}" '{x=down*$2; y=down*$3; printf "%10i%10i%12s\n", x, y, "1.0"}' >> ${coordfile} | |||
end | |||
rm -f tt.dat | |||
echo "Done!" | |||
else | |||
else | echo "Usage: " $0 "<input xmd file> <tablename> <downsamplefactor>" | ||
echo "Run this script in the directory where all your mrc micrographs are" | |||
endif | |||
endif | |||
=== Notes === | |||
* The tablename is the name that XMIPP3 has given to the STAR-file table with all the images, e.g. data_noname or data_class000001_images. | |||
* The downsample factor is the one you used in XMIPP3 to extract your particles. | |||
* If you run this script in the Micrographs directory, the coordinate files will already be in their correct position. |
Latest revision as of 13:25, 13 November 2017
#!/usr/bin/env csh # # if ($# == 3 ) then set xmdfile = $1 set tablename = $2 set downsample = $3 relion_star_printtable ${xmdfile} ${tablename} _micrograph _xcoor _ycoor | awk -F"/" '{print $NF}' | sort > tt.dat foreach mic (`cat tt.dat | awk '{print $1}' | uniq`) set coordfile=`echo ${mic} | sed 's|.mrc|.coord|'` echo "Creating " $coordfile " ... " echo " x y density" > ${coordfile} grep ${mic} tt.dat | awk -v"down=${downsample}" '{x=down*$2; y=down*$3; printf "%10i%10i%12s\n", x, y, "1.0"}' >> ${coordfile} end rm -f tt.dat echo "Done!" else echo "Usage: " $0 "<input xmd file> <tablename> <downsamplefactor>" echo "Run this script in the directory where all your mrc micrographs are" endif
Notes
- The tablename is the name that XMIPP3 has given to the STAR-file table with all the images, e.g. data_noname or data_class000001_images.
- The downsample factor is the one you used in XMIPP3 to extract your particles.
- If you run this script in the Micrographs directory, the coordinate files will already be in their correct position.