Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells REFINEMATCH(1) REFINEMATCH(1) NAME refinematch - Solve for a refined match between two tomograms SYNOPSIS refinematch [options] input_file [output_file] DESCRIPTION Refinematch will solve for a general 3-dimensional linear transformation to align two volumes to each other. It performs multiple linear regression on the displacements between the volumes determined at a matrix of positions. The displacements must be contained in a file with the following form: Number of displacements One line for each displacement consisting of the X, Y, and Z coordinates in the first volume, then the displacements in X, Y and Z involved in moving from the first to the second volume The program will automatically eliminate "outliers", patch displacements that are likely to be incorrect because they are so extreme, when compared to the rest of the displacements. This elimination is conservative, but if for some reason it operates incorrectly, you can control the parameters of elimination or stop the elimination from occurring. The program will eliminate up to 10% of the patches. If more than this number are bad, either get a new set of patches that do not approach so close to the edge of the volume, make a model in the tomogram with contours enclosing the patches to use, eliminate the bad ones from the file by hand, or use Findwarp to eliminate a whole row or column of patches. When the mean residual exceeds a value that you specify, the program will exit with an error. A model specifying which patches to include in the fit can be quite simple, consisting of just a single contour enclosing the region where patches are generally good. This contour can be drawn in any Z plane of the flipped tomogram. However, if the good region changes through the depth of the tomogram, you can draw contours at several Z levels. If you have two layers of patches, draw two contours, one near the top and one near the bottom of the tomogram; if you have three layers, add another contour in the middle, etc. For a given patch, the program will find the contour at the nearest Z level and use that one to determine whether to include the patch. If there is only one layer of patches in one dimension, there is insufficient information to solve for the full transformation, so the program will solve for only two of the three columns of the transformation matrix. This typically occurs in the Y dimension, in which case the second column of the matrix is fixed at 0, 1, 0. Refinematch uses the PIP package for input (see the manual page for pip) but can still take input interactively for compatibility with old versions of Matchorwarp. The following options can be specified either as command line arguments (with the -) or one per line in a command file or parameter file (without the -): -patch OR -PatchFile File name Name of input file with positions and displacements. If this option is not entered, the first non-option argument will be used for the input file name. -output OR -OutputFile File name Optional output file for the refining transformation. If this option is not entered, the second non-option argument (if any) will be used for the output file name. -region OR -RegionModel File name Model file with contours enclosing the patches to be included in the fit -volume OR -VolumeOrSizeXYZ File name Either the name of the file or the X, Y, and Z dimensions of the volume being matched to. -residual OR -ResidualPatchOutput File name Output file for positions, displacements, and residual values. If the patch input file has correlation coefficients, they will be replaced by the residuals. -reduced OR -ReducedVectorOutput File name Output file for residual vectors from the fit, which represent the vectors remaining after removing the linear component of the vector field. These are referred to as reduced vectors. If the input patch file has correlation coefficients, they will be passed into this output file; otherwise the residual values will be placed into the file. -limit OR -MeanResidualLimit Floating point Limiting value for the mean residual; above this value, the program will exit with an error. -maxfrac OR -MaxFractionToDrop Floating point Maximum fraction of patches to drop from the fit by outlier elimination. Enter 0 to for no outlier elimination. The default is 0.1. -minresid OR -MinResidualToDrop Floating point The minimum residual for outlier elimination; patches with residuals smaller than this value will be retained no matter how extreme they are relative to the other patches. The default is 0.5. -prob OR -CriterionProbabilities Two floats Two probabilities controlling outlier elimination: a criterion probability for a patch to be evaluated as an outlier (default 0.01), and a criterion probability for a patch to be eliminated regardless of the distribution of extreme values (default 0.002). -param OR -ParameterFile Parameter file Read parameter entries as keyword-value pairs from a parameter file. -help OR -usage Print help output -StandardInput Read parameter entries from standard input. If the program is started with no command line arguments, it takes interactive input with the following entries: Name of file with positions and displacements Either the file name, or the X, Y, and Z dimensions of the volume being matched to. Name of an IMOD model file with contours enclosing the patches to be included in the fit, or Return to use all patches. Limiting value for the mean residual; above this value, the program will exit with an error. Name of output file in which to place the transformation, or Return for no output to a file HISTORY Written by David Mastronarde, 1995 12/24/98: added outlier elimination; 6/6/99: added error exit 8/21/06: converted to PIP, made it handle both orientations of volume better, changed outlier output to be a summary as in Findwarp, added options for controlling outlier elimination and getting residual output.