refinematch(1) General Commands Manual refinematch(1)NAMErefinematch - Solve for a refined match between two tomogramsSYNOPSISrefinematch [options] input_file [output_file]DESCRIPTIONRefinematch will solve for a general 3-dimensional linear transforma- tion 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 displace- ments that are likely to be incorrect because they are so extreme, when compared to the rest of the displacements. This elimination is conser- vative, 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 con- tours 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 deter- mine whether to include the patch. If there is only one layer of patches in one dimension, there is insuf- ficient information to solve for the full transformation, so the pro- gram 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.OPTIONSRefinematch 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 com- mand file or parameter file (without the -). Options can be abbrevi- ated to unique letters; the currently valid abbreviations for short names are shown in parentheses.-patch(-pat)OR-PatchFileFilenameName 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(-o)OR-OutputFileFilenameOptional 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(-reg)OR-RegionModelFilenameModel file with contours enclosing the patches to be included in the fit-volume(-v)OR-VolumeOrSizeXYZFilenameEither the name of the file or the X, Y, and Z dimensions of the volume being matched to.-residual(-res)OR-ResidualPatchOutputFilenameOutput file for positions, displacements, and residual values. If the patch input file has correlation coefficients, they will be replaced by the residuals.-reduced(-red)OR-ReducedVectorOutputFilenameOutput 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(-l)OR-MeanResidualLimitFloatingpointLimiting value for the mean residual; above this value, the pro- gram will exit with an error.-extra(-e)OR-ExtraValueSelectionTwointegersSelect only patches with extra value on one side of a criterion. The patch vector file can have additional columns of values after the displacements in X, Y, and Z. These extra columns are numbered from 1, and they may also have ID values on the first line of the file indicating their type. To include patches based on values in an extra column, enter two numbers for this option: the ID value or the negative of the extra column number; and 1 to select patches above the criterion or -1 to select ones below it. You must also enter one or more threshold values with the-selectoption. (Successive entries accumulate)-select(-se)OR-SelectionCriteriaMultiplefloatsOne or more criteria for selecting patches based on extra val- ues. If multiple criteria are entered, the fitting process will be repeated with each selection criterion to try to satisfy the residual criterion. If there are multiple values being selected on, this option must be entered the same number of times as the-extraoption and it must have the same number of criteria entered each time. (Successive entries accumulate)-maxfrac(-ma)OR-MaxFractionToDropFloatingpointMaximum fraction of patches to drop from the fit by outlier elimination. Enter 0 to for no outlier elimination. The default is 0.1.-minresid(-mi)OR-MinResidualToDropFloatingpointThe 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.-probOR-CriterionProbabilitiesTwofloatsTwo 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).-initial(-i)OR-InitialTransformFileFilenameFile with the 3D transformation that was used to create the vol- ume being aligned. This transformation will be multiplied by the refining transform and output in the file specified by the-productoption. The two options must be entered together. A side-effect of using this option is that the program will report the shift in Y (the presumed depth dimension) needed to align corresponding patches in the center of the volumes.-product(-prod)OR-ProductTransformFileFilenameName of output file for the product of the transform entered with the-initialoption and the refining transform.-scale(-sc)OR-ScaleShiftByFactorFloatingpointFactor by which to scale shifts in the transform written when the-productoption is given. This option is needed to get a transformation that can be applied to an unbinned volume when binned volumes have been analyzed.-param(-par)OR-ParameterFileParameterfileRead parameter entries as keyword-value pairs from a parameter file.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.INTERACTIVEINPUTIf 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 fileHISTORYWritten 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.BUGSEmail bug reports to mast at colorado dot edu. IMOD 4.11.0 refinematch(1)