taperoutvol(1)              General Commands Manual             taperoutvol(1)

       taperoutvol - to excise a subset of a volume, taper and pad outside

       taperoutvol  [options]  input_file  output_file

       Taperoutvol will cut a subset out of an image volume, pad it into a
       larger volume, and taper the intensity down to the mean value of the
       volume over the extent of the padding region, i.e., from the edge of
       the actual excised pixels to the edge of the new volume.  None of the
       original excised pixels are attenuated by this method.  The resulting
       volume will have dimensions suitable for taking the FFT unless the
       -nofft option is entered.  Its origin will be set so that a model built
       on this subvolume in 3dmod should load correctly on the full volume.

       Taperoutvol uses the PIP package for input (see the manual page for
       pip) and can still take sequential input interactively, to maintain
       compatibility with old command files.  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 parentheses.

       -input (-i) OR -InputFile      File name
              Input image file

       -output (-o) OR -OutputFile    File name
              Output image file

       -xminmax (-x) OR -XMinAndMax   Two integers
              Starting and ending X index coordinates to extract, numbered
              from 0.  The default is the whole width in X.

       -yminmax (-y) OR -YMinAndMax   Two integers
              Starting and ending Y index coordinates to extract, numbered
              from 0.  The default is the whole height in Y.

       -zminmax (-z) OR -ZMinAndMax   Two integers
              Starting and ending Z index coordinates to extract, numbered
              from 0.  The default is the whole depth in Z.

       -taper (-t) OR -TaperPadsInXYZ      Three integers
              Number of pixels over which to taper and pad the patches in X, Y
              and Z.  The default is 0.  Unless the -nofft option is entered,
              the amount of tapering in any dimension may be increased to make
              that dimension suitable for taking an FFT.

       -nofft (-nof) OR -NoFFTSizes
              Do not adjust the padding to give sizes suitable for an FFT.
              This option is particularly important if you want no tapering
              and padding.

       -noise (-noi) OR -NoisePadding
              Use tapered noise based on nearby pixels along the edge of an
              image to pad the images.  The default is to pad with a simple
              taper that makes streaks outside the edge of the image.

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter

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

              Read parameter entries from standard input.

       If there are no command-line arguments, Taperoutvol takes sequential
       input the old way, with the following entries:

       Inputs to the program:

       Name of input file

       Name of output file

       The starting and ending X index coordinates (number from 0), the start-
       ing and ending Y index coordinates, and the starting and ending Z index
       coordinates to extract.  The default is the whole volume.

       The width of the borders, in X, Y, and Z, with which to pad the image
       block.  Borders will be made larger as necessary to make the output
       image size suitable for taking a 3D FFT, with the exception that if a
       single Z slice is requested with no padding, only a single slice is
       produced without padding.

       The program will stop with an error message if memory cannot be allo-
       cated for the output image, or if the subset is not entirely within the
       input volume.

       Written by David Mastronarde  3/1/01
       Converted to PIP, 1/8/10

       Email bug reports to mast at colorado dot edu.

IMOD                                4.10.10                     taperoutvol(1)