matchorwarp(1)              General Commands Manual             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 -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -inputvolume (-inp) OR -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 (-o) OR -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 (-si) OR -SizeXYZorVolume     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 (-refinel) OR -RefineLimit       Floating point
              The maximum mean residual that will be allowed when running
              Refinematch and Matchvol.

       -warplimit (-warpl) OR -WarpLimits       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.

       -structurecrit (-st) OR -StructureCriteria    Text string
              A list of one or more criterion values for selecting patches
              based on a measure of structure contained in the patch file.
              Both Refinematch and Findwarp will be run with these lim-
              its for selecting patches with the structure value greater than
              the criterion.  In Findwarp, each criterion will be applied
              at a mean residual limit before going on to the next residual
              limit.  The measure of structure will be the fraction of ana-
              lyzed boxes within a patch with a standard deviation indicative
              of a strong structure, which is saved in the patch file by
              Corrsearch3d as an extra column with ID 5.

       -extentfit (-e) OR -ExtentToFit     File name
              Minimum number of rows and columns of patches to include in each
              local fit in Findwarp.

       -modelfile (-m) OR -ModelFile       File name
              Name of a model file with contours enclosing the patches to
              include in fits.

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

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

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

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

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

       -residualfile (-res) OR -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 (-v) OR -VectorModel   File name
              Name of patch vector model file to create from the residual file
              with Patch2imod.

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

       -tempdir (-te) OR -TemporaryDirectory    File name
              Path name of directory into which Matchvol or Warpvol can place
              temporary files.

       -xlowerexclude (-xl) OR -XLowerExclude   Integer
              The number of columns of patches to exclude on the left side of
              the volume.

       -xupperexclude (-xu) OR -XUpperExclude   Integer
              The number of columns of patches to exclude on the right side of
              the volume.

       -ylowerexclude (-yl) OR -YLowerExclude   Integer
              The number of rows or slabs of patches to exclude on the lower Y
              side of the volume.

       -yupperexclude (-yu) OR -YUpperExclude   Integer
              The number of rows or slabs of patches to exclude on the upper Y
              side of the volume.

       -zlowerexclude (-zl) OR -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 (-zu) OR -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 (-l) OR -LinearInterpolation
              Use linear instead of quadratic interpolation for transforming
              the volume with Matchvol or Warpvol.

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

       -help (-h) OR -usage
              Print help output

       -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



IMOD                                4.10.10                     matchorwarp(1)