binvol(1)                   General Commands Manual                  binvol(1)

       binvol - Reduce a 3D volume in size isotropically or anisotropically

       binvol  [options]  input_file  output_file

       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.

       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, 2 for 32-bit
              floating point, or 12 for 16-bit floating point.  Floating point
              would be useful to preserve intensity 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, although the default mode of
              floating point output for MRC files is governed by the value of
              environment variable IMOD_WRITE_FLOATS_16BIT..  Mode 12 is
              allowed only if the output format is MRC.

       -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-
                  2: Blackman - fast but not as good at antialiasing as slower
                  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

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

              Read parameter entries from standard input.

       Written by David Mastronarde
       Converted to PIP input and added to package, 10/28/04

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.35                          binvol(1)