tomopieces(1) General Commands Manual 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, the amount of overlap to generate
between the extracted pieces, and whether output is to be written
directly to a chunked HDF file.
Its first line of output is the number of pieces in X, Y, and Z. For a
normal output file, this is followed by the starting and ending index
coordinates in X, Y, and Z required for extracting each piece with Tap-
eroutvol, then three lines with the index coordinates required for
putting the pieces back together with Assemblevol (first the X coordi-
nates for each position in X, then the Y coordinates for each position
in Y, then the Z coordinates for each position in Z). For a chunked
HDF file, there are two output line for each piece: one with X, Y, and
Z coordinates to extract, then one with the starting and ending X, Y,
and Z indexes in the padded chunk of data to write out, and the X, Y,
and Z coordinates at which to write the chunk in the output file.
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 80)
-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 100. 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 100. 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 100.
-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)
-hdf (-hd) OR -ChunksForHDF
Set up for direct output to a chunked HDF file. The program
will generate equally spaced chunks on each axis with a size
that minimizes the wasted space in the last chunk.
-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 (-he) 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.
IMOD 4.11.0 tomopieces(1)