matchorwarp(1)                                                  matchorwarp(1)



NAME
       matchorwarp - Find registration between two volumes and transform one

SYNOPSIS
       matchorwarp [options] <input file>  <output file>

DESCRIPTION
       Matchorwarp runs Refinematch to attempt to find a single linear
       transformation relating two volumes.  If a single transformation gives
       an adequate fit, Matchorwarp runs Matchvol to generate the output
       file from the input file.  Otherwise, it runs Findwarp to find a set
       of warping transformations that relate the two volumes.  If an adequate
       fit is found, it then runs Warpvol to generate the input file from
       the output file; otherwise it exits with an error.  There are options
       to run Matchorwarp in a trial mode and to exclude rows or columns of
       patches, so this program can be used to explore different fits before
       or instead of running Findwarp interactively.

   Options
       Give the command "matchorwarp" without arguments to see a list of the
       current defaults for many of these options.  Options may be abbreviated
       to the minimum number of unambiguous characters.

       Matchorwarp 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 -):

       -InputVolume    File name
              Input file to be transformed.  If this option is not entered,
              the first nonoption argument is taken as the input volume.

       -OutputVolume   File name
              Name of transformed file to be produced.  If this option is not
              entered, the second nonoption argument is taken as this name.

       -size      Text string
              Specifies the size of the volume being matched to; the entry can
              be either the name of that file or its NX,NY,NZ dimensions.

       -refinelimit    Floating point
              The maximum mean residual that will be allowed when running
              Refinematch and Matchvol.

       -warplimit      Text string
              A list of mean residuals that Warpvol will attempt to achieve
              automatically.  Values should be in increasing order and sepa-
              rated by commas.

       -modelfile      File name
              Name of a model file with contours enclosing the patches to
              include in fits.

       -patchfile      File name
              Name of the existing file with list of patch displacements
              (default patch.out).

       -solvefile      File name
              Name of the existing file with the initial transformation
              between volumes (default solve.xf).

       -refinefile     File name
              Name of the file into which Refinematch will place the refin-
              ing transformation (default refine.xf).

       -inversefile    File name
              Name of the file into which Matchvol will place the inverse
              cumulative transformation (default inverse.xf).

       -warpfile       File name
              Name of the file into which Warpvol will place the inverse
              warping transformations (default warp.xf).

       -residualfile   File name
              Name of the file into which Refinematch and/or Warpvol
              will place a new list of the patches, their displacements, and
              the residual from the fits.

       -vectormodel    File name
              Name of patch vector model file to create from the residual file
              with Patch2imod.

       -clipsize       Integer
              If writing a patch vector model, set up four clipping planes
              enclosing a square central area of the given size.

       -tempdir   File name
              Path name of directory into which Matchvol or Warpvol can place
              temporary files.

       -xlowerexclude       Integer
              The number of columns of patches to exclude on the left side of
              the volume.

       -xupperexclude       Integer
              The number of columns of patches to exclude on the right side of
              the volume.

       -ylowerexclude       Integer
              The number of rows or slabs of patches to exclude on the lower Y
              side of the volume.

       -yupperexclude       Integer
              The number of rows or slabs of patches to exclude on the upper Y
              side of the volume.

       -zlowerexclude       Integer
              The number of slabs or rows of patches to exclude on the lower Z
              side of the volume.  This would be used to specify rows on the
              bottom when viewing a volume in flipped orientation.

       -zupperexclude       Integer
              The number of slabs or rows of patches to exclude on the upper Z
              side of the volume.  This would be used to specify rows on the
              top when viewing a volume in flipped orientation.

       -linear
              Use linear instead of quadratic interpolation for transforming
              the volume with Matchvol or Warpvol.

       -trial Use a trial mode, in which the program exits after finding a
              good fit rather than going on to Matchvol or Warpvol.

       -StandardInput
              Read parameter entries from standard input


FILES
       Unless optional arguments are entered, the program assumes the exis-
       tence of patch.out and solve.xf.

AUTHOR
       David Mastronarde  <mast at colorado dot edu>

SEE ALSO
       patchcrawl3d, refinematch, matchvol, findwarp, warpvol,
       patch2imod



BL3DEMC                              4.5.6                      matchorwarp(1)