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)