tomopieces(1) General Commands Manual tomopieces(1)NAMEtomopieces - compute pieces for combining tomogramsSYNOPSIStomopieces [options] filenameDESCRIPTIONTomopieces figures out how to chop up a tomogram into pieces so that the Fourier transforms or other operations on each piece can be done in memory. It makes its decisions based on the maximum number of voxels that should be included in each piece. For typical processing, such as for taking an FFT, the memory consumed will be about four times the number of voxels, since data are typically stored in memory as real numbers. The program chooses a division of the volume that minimizes the total surface area of the extracted pieces, subject to specified constraints on the number of pieces in each dimension. Its one required input is the name of the tomogram file. Optional inputs specify the maximum number of voxels, the maximum number of pieces to extract in each dimension, the border sizes for padding (and tapering) the extracted pieces, and the amount of overlap to generate between the extracted pieces. It outputs the number of pieces in X and Z, the index coordinates in X, Y, and Z required for extracting each piece with Taperoutvol, and the index coordinates required for putting the pieces back together with Assemblevol (first the X coordinates for each position in X, then the Y coordinates for each position in Y, then the Z coordinates for each position in Z).OPTIONSTomopieces uses the PIP package for input (see the manual page for pip). 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 -). Options can be abbreviated to unique letters; the currently valid abbreviations for short names are shown in paren- theses.-tomogram(-t)OR-TomogramOrSizeXYZFilenameInput file to be cut up, or the dimensions in X, Y and Z-megavox(-me)OR-MegaVoxelsFloatingpointMaximum number of megavoxels to allow in each piece (default 20)-xpad(-xp)OR-XPaddingIntegerNumber of pixels to pad on each side in X (default 8)-ypad(-yp)OR-YPaddingIntegerNumber of pixels to pad on each side in Y (default 4)-zpad(-zp)OR-ZPaddingIntegerNumber of pixels to pad on each side in Z (default 8)-xmaxpiece(-xm)OR-XMaximumPiecesIntegerMaximum number of pieces in X. Enter -1 for essentially no con- straints (a maximum of X image size divided by 2). The default is 0 for X and Y, which will make the total number of pieces in X and Y be no more than 19. If the maximum for Y is set to 1, a value of 0 for X will make the number of pieces in X be no more than 19. These constraints will allow Assemblevol to keep all files in one layer in Z open at once.-ymaxpiece(-ym)OR-YMaximumPiecesIntegerMaximum number of pieces in Y. Enter -1 for essentially no con- straints (a maximum of Y image size divided by 2). The default is 0; see entry for XMaximumPieces. If the maximum for X is set to 1, a value of 0 for Y will make the number of pieces in Y be no more than 19.-zmaxpiece(-zm)OR-ZMaximumPiecesIntegerMaximum number of pieces in Z. The default is -1 for essen- tially no constraints (a maximum of Z image size divided by 2).-minoverlap(-mi)OR-MinimumOverlapIntegerMinimum number of pixels to overlap between pieces (default 4)-nofft(-n)OR-NoFFTSizesDo not adjust the padding to give sizes suitable for an FFT. If this option is entered, be sure that it is also sent to Taper- outvol(1).-param(-p)OR-ParameterFileParameterfileRead parameter entries as keyword-value pairs from a parameter file.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.HISTORYWritten by David Mastronarde; revised for pieces in X 3/1/01 Converted to PIP input and generalized to 3 dimensions, 6/14/04BUGSEmail bug reports to mast at colorado dot edu. IMOD 4.10.22 tomopieces(1)