binvol(1) General Commands Manual binvol(1)
NAME
binvol - Reduce a 3D volume in size isotropically or anisotropically
SYNOPSIS
binvol [options] input_file output_file
DESCRIPTION
Binvol will bin down a volume in all three dimensions, with the binning
done isotropically or by different amounts in X, Y, and Z. Binning
means summing (actually averaging) all of the values in a block of vox-
els (e.g., 2x2x2 or 1x1x3) in the input volume to create one voxel in
the output volume. The output file will have appropriately larger
pixel spacings in its header. It is also possible to use antialiased
image reduction instead of binning in Z, as well as in X and Y when the
reduction is equal in X and Y.
OPTIONS
Binvol 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 (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-i) OR -InputFile File name
Input image file to bin down in 3D
-output (-o) OR -OutputFile File name
Output file for binned volume
-mode (-mo) OR -ModeToOutput Integer
The storage mode of the output file; 0 for byte, 1 for 16-bit
signed integer, 6 for 16-bit unsigned integer, or 2 for 32-bit
floating point. The latter would be useful to preserve inten-
sity resolution in the averaged data, particularly important
when applying a large amount of binning to relatively small byte
or integer values. The default is the mode of the input file.
-binning (-b) OR -BinningFactor Integer
Overall reduction factor to bin by (default 2)
-xbinning (-x) OR -XBinningFactor Integer
Factor to bin by in X (default same as overall factor)
-ybinning (-y) OR -YBinningFactor Integer
Factor to bin by in Y (default same as overall factor)
-zbinning (-z) OR -ZBinningFactor Integer
Factor to bin by in Z (default same as overall factor)
-antialias (-a) OR -AntialiasZFilter Integer
The Z dimension will be reduced with antialiased filtering
instead of with binning if a number between 2 and 6 is entered
to specify the filter type. If the binning is equal in X and Y
(and greater than 1), then antialiased reduction will be applied
in those dimensions as well, even if it is different from the Z
binning. The result will be slightly shifted from that obtained
with the -shrink option to Newstack if the X or Y dimension
is not a multiple of the binning. The filters are as in New-
stack(1):
2: Blackman - fast but not as good at antialiasing as slower
filters
3: Triangle - fast but smooths more than Blackman
4: Mitchell - good at antialiasing, smooths a bit
5: Lanczos 2 lobes - good at antialiasing, less smoothing
than Mitchell
6: Lanczos 3 lobes - slower, even less smoothing but more
risk of ringing
-spread (-s) OR -SpreadSlicesInZ
Output slices in Z that sample, or are centered on, Z values as
close to the starting and ending input slices as possible. This
option can be used only when doing antialiased reduction in Z.
By default, the first output slice is centered on the middle of
the first set of slices corresponding to the binning in Z. The
bottom edge of this slice is the same as the bottom edge of the
first input slice and the Z origin is unchanged. With this
option, the centering of the first slice may be moved down, and
the Z origin will be increased to adjust for this.
-memory (-me) OR -MemoryLimit Integer
Maximum size of working array in megabytes. The size of the
array determines whether data are read in and binned in chunks
or as whole slices, which is more efficient. The default is
1000; the value cannot be bigger than 8000.
-verbose (-v) OR -VerboseOutput Integer
Output debugging information: 1 for basic, 2 for output per
slice
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde
Converted to PIP input and added to package, 10/28/04
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 binvol(1)