Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells MATCHVOL(1) MATCHVOL(1) NAME matchvol - transform a volume to match another with a general linear transformation SYNOPSIS matchvol DESCRIPTION Matchvol will transform a volume using a general linear transformation. Its main use is to transform one tomogram from a two-axis tilt series so that it matches the other tomogram. To do so, it can combine an initial alignment transformation and any number of successive refining transformations. The program uses the same algorithm as Rotatevol for rotating large volumes. The format of the 3D transform when stored in a file is to consist of 3 lines: a11 a12 a13 dx a21 a22 a23 dy a31 a32 a33 dz which specify a transformation for getting from a location in the input volume to a location in the output volume: xo = a11 * xi + a12 * yi + a13 * zi + dx yo = a21 * xi + a22 * yi + a23 * zi + dy zo = a31 * xi + a32 * yi + a33 * zi + dz where (xo, yo, zo) are coordinates relative to the center of the output volume, and (xi, yi, xi) are coordinates relative to the center of the input volume. Matchvol uses the PIP package for input (see the manual page for pip) and can take input interactively for options that existed when it was converted, to maintain compatibility with old command files. 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 -): -input OR -InputFile File name Input image file to transform -output OR -OutputFile File name Output file for transformed volume -inverse OR -InverseFile File name Output file in which to write the inverse of the combined transformation. This output is optional. -tempdir OR -TemporaryDirectory Text string Directory to use for temporary files. The default is that the temporary files will be placed in the current directory. -size OR -OutputSizeXYZ Three integers X, Y, Z dimensions of the output file (Default is size of input file) -center OR -CenterXYZ Three floats X, Y, Z index coordinates of the center of the region to transform (Default is center of input file). Coordinates are numbered from zero. -xffile OR -TransformFile File name Name of file with 3D transform to apply. Multiple transforms are applied in the order that they are entered, and before any 3DTransform entries. (Successive entries accumulate) -3dxform OR -3DTransform Multiple floats A 3D transform to apply, consisting of 12 values on one line (a11, a12, a13, dx, a21, a22, a23, dy, a31, a32, a33, dz). Multiple transforms are applied in the order that they are entered, and after any 3DTransform entries. (Successive entries accumulate) -order OR -InterpolationOrder Integer Order of interpolation to use. Currently only quadratic (2) and linear (1) interpolation are available; the default is quadratic. -memory OR -MemoryLimit Integer Amount of memory to allocate for the major arrays needed by the program. This always includes memory for input images and may include memory for a stack of output slices, depending on the orientation of the output. -verbose OR -VerboseOutput Integer 1 for diagnostic output -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 reverts to interactive input with the following entries: Name of the input file to be transformed Name of the output file for the transformed volume Path name of directory (for example, /usr/tmp) where temporary files can be placed, or Return to have files placed in the current directory X, Y, and Z dimensions of the output file, or / to accept the default values, which are NZ, NY, and NX of the input volume (a 90-degree rotation about the Y axis) Number of successive transformations to combine and apply For each transformation, either enter the name of a file with the transformation, or enter a Return, then enter the 12-element transformation directly. Transform files need not all occur before direct entries. Name of a file in which to place the inverse of the combined transformation, or Return for no such output HISTORY Written by David Mastronarde, 1995 Converted to PIP/autodoc 10/10/03 Converted to Fortran 95, parallelized with OpenMP, 6/14/09