tomopieces(1)                                                    tomopieces(1)



NAME
       tomopieces - compute pieces for combining tomograms

SYNOPSIS
       tomopieces  [options]  filename

DESCRIPTION
       Tomopieces 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).

OPTIONS
       Tomopieces 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 -TomogramOrSizeXYZ     File name
              Input file to be cut up, or the dimensions in X, Y and Z

       -megavox (-me) OR -MegaVoxels       Floating point
              Maximum number of megavoxels to allow in each piece (default 20)

       -xpad (-xp) OR -XPadding       Integer
              Number of pixels to pad on each side in X (default 8)

       -ypad (-yp) OR -YPadding       Integer
              Number of pixels to pad on each side in Y (default 4)

       -zpad (-zp) OR -ZPadding       Integer
              Number of pixels to pad on each side in Z (default 8)

       -xmaxpiece (-xm) OR -XMaximumPieces      Integer
              Maximum 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 -YMaximumPieces      Integer
              Maximum 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 -ZMaximumPieces      Integer
              Maximum 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 -MinimumOverlap     Integer
              Minimum number of pixels to overlap between pieces (default 4)

       -nofft (-n) OR -NoFFTSizes
              Do 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 -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter
              file.

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.

HISTORY
          Written by David Mastronarde; revised for pieces in X 3/1/01
          Converted to PIP input and generalized to 3 dimensions, 6/14/04

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                       tomopieces(1)