Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

TAPEROUTVOL(1)							 TAPEROUTVOL(1)

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

SYNOPSIS
  taperoutvol

DESCRIPTION
  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 -):

 -input OR -InputFile   File name
    Input image file

 -output OR -OutputFile   File name
    Output image file

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

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

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

 -taper 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 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.

 -param OR -ParameterFile   Parameter file
    Read parameter entries as keyword-value pairs from a parameter file.

 -help OR -usage
    Print help output

  -StandardInput
     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
  starting 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 allocated
  for the output image, or if the subset is not entirely within the input 
  volume.
  
HISTORY
  Written by David Mastronarde  3/1/01
  Converted to PIP, 1/8/10