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 4.3.7 matchorwarp(1)