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 -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -name (-na) OR -RootName       File name
              Root name of dataset, excluding a and b

       -atob (-a) OR -MatchAtoB
              Match A to B instead of B to A

       -tolist (-to) 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 (-f) 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 (-tr) OR -TransferPointFile    File name
              File of matching fiducial coordinates produced by running trans-
              ferfid with the -c option.

       -uselist (-use) OR -UsePointList    List of integer ranges
              List of starting points to use from the A axis in Solvematch

       -surfaces (-s) 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 (-p) 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 (-x) 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 (-y) 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 (-z) OR -ZLowerAndUpper    Two integers
              Lower and upper coordinate limits of patches in Z.  There is no
              default; these limits must be entered.

       -regionmod (-r) OR -PatchRegionModel     File name
              Model with contours enclosing regions to do patch correlations
              in.  The same model will be supplied to Matchorwarp.

       -tempdir (-te) 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 (-no) 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 (-h) 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                              4.7.3                     setupcombine(1)