setupcombine(1) setupcombine(1) NAME setupcombine - Create command files for combining dual-axis tomograms SYNOPSIS setupcombine [options] -name rootname DESCRIPTION Setupcombine generates the command files needed to combine two single- axis tomograms into one. These files include solvematch.com, matchvol1.com, patchcorr.com, matchorwarp.com, volcombine.com, and com- bine.com, which are all used for processing in eTomo. Files matchvol2.com and warpvol.com are also created and could be used at the command line instead of the matchorwarp step. Options Setupcombine uses the PIP package for input (see the manual page for pip). Options can be specified either as command line arguments (with the -) or one per line in a command file (without the -): -name OR -RootName File name Root name of dataset, excluding a and b -atob OR -MatchAtoB Match A to B instead of B to A -tolist OR -ToVolPointList List of integer ranges List of points in tomogram being matched to that have corre- sponding points, used to provide the entry to Solvematch for ACorrespondenceList. -fromlist OR -FromVolPointList List of integer ranges List of corresponding points in tomogram being transformed to match, used to provide the entry to Solvematch for BCorrespon- denceList. -transfer OR -TransferPointFile File name File of matching fiducial coordinates produced by running trans- ferfid with the -c option. -uselist OR -UsePointList List of integer ranges List of starting points to use from the A axis in Solvematch -surfaces OR -SurfaceModelType Integer This entry provides the SurfacesOrUseModels entry for Solve- match. Enter 0 to use matching models and fiducials if any, 2 for fiducials distributed in Z (e.g. on two surfaces), 1 or -1 for fiducials on one surface (-1 if tomograms are inverted in Z with respect to each other), or -2 to use matching models only. -patchsize OR -PatchTypeOrXYZ Text string Enter a letter to indicate the size of patches, or three numbers for the desired size in X, Y, and Z. The sizes available by letter are S for small (64x32x64), M for medium (80x40x80), L for large (100x50x100), or E for extra large (120x60x120). -xlimits OR -XLowerAndUpper Two integers Lower and upper coordinate limits of patches in X. The default limits exclude a border that varies from 24 pixels for the shorter tomogram dimension under 1000 pixels to 80 pixels for the shorter tomogram dimension above 4000 pixels. -ylimits OR -YLowerAndUpper Two integers Lower and upper coordinate limits of patches in Y. The default limits exclude a border that is the same as for the X limits just described. -zlimits OR -ZLowerAndUpper Two integers Lower and upper coordinate limits of patches in Z. There is no default; these limits must be entered. -regionmod OR -PatchRegionModel File name Model with contours enclosing regions to do patch correlations in. The same model will be supplied to Matchorwarp. -tempdir OR -TemporaryDirectory File name Location to create a temporary local directory. This directory will be used for the transformed volumes, the temporary files created during volume transformations, and the chunks of the combined volume. -noclean OR -NoTempCleanup Do not clean up the temporary directory when finished. This option allows you to examine the transformed volume after the operation is completed. The default is to remove the temporary directory and its contents when the combine operation completes. -help OR -usage Print help output -StandardInput Read parameter entries from standard input FILES All files are modified from the master files in the $IMOD_DIR/com directory. Existing copies of the command files will be made into backup files by adding the extension ~. AUTHOR David Mastronarde BUGS Email bug reports to mast at colorado dot edu SEE ALSO solvematch, corrsearch3d, matchorwarp, combinefft, dens- match(1), filltomo HISTORY Setupcombine was a originally a C-shell script. In December 2010 it was converted to Python. BL3DEMC 4.3.7 setupcombine(1)