Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

SUBIMAGE(1)							 SUBIMAGE(1)

NAME
	subimage - subtracts one image from another

SYNOPSIS
	subimage [options] input_file_A input_file_B output_file

DESCRIPTION

  Subimage will subtract one image from another, or a series of images from one
  file from a series in another file.  It will report the minimum, maximum,
  mean, and standard deviation of each difference image.

  Subimage uses the PIP package for input (see the manual page for pip)
  and can still take sequential input interactively.  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 -):

 -afile OR -AFileSubtractFrom   File name
    Input image file to subtract images from (file A).  If this option is not
    entered, the first non-option argument will be used for this input file.

 -bfile OR -BFileSubtractOff   File name
    Input image file B with images to subtract from A.  If this option is not
    entered, the second non-option argument will be used for this input file,
    if it exists.  If this file is not specified at all, a backup file to A
    will be used (the A filename with ~ appended).

 -output OR -OutputFile   File name
    Output file C for difference images.  If this option is not entered, the
    third non-option argument will be used for this output file, if it exists.
     If this file is not specified at all, only statistics will be reported
    for each section.

 -mode OR -ModeOfOutput   Integer
    Mode for output file (1 for integers, 2 for floating point).  Bytes (mode
    0) are rarely suitable for a difference image since they are unsigned.

 -asections OR -ASectionList   List of integer ranges
    List of sections in file A (numbered from 0, default is all sections)

 -bsections OR -BSectionList   List of integer ranges
    List of sections in file B.  Sections are numbered from 0.  The default is
    to use the first N sections in the file, where N is the number of sections
    in the list for file A.

 -zero OR -ZeroMeanOutput
    Make the mean of the output be zero for each section by subtracting the
    mean difference between sections from the difference.

 -lower OR -LowerThreshold   Floating point
    Truncate the output by replacing values below this theshold with the
    threshold value.

 -upper OR -UpperThreshold   Floating point
    Truncate the output by replacing values above this theshold with the
    threshold value.

 -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, Subimage takes sequential input
  the old way, with the following entries:

  Image file A

  List of section numbers for the images from file A; ranges may be entered,
       or / for all sections in the file

  Image file B, or a blank line to use the backup of file A (A~).

  List of corresponding section numbers for the images from file B; again,
        ranges may be entered, and / will sections from the beginning of the
        file

  Output file for difference A minus B, or a blank line for no output file,
        if only statistics are desired

HISTORY
  Written by Sam Mitchell, 2/8/89
  Revised by David Mastronarde to do multiple sections, 11/4/00
  Revised by David Mastronarde to provide statistics and omit output file,
       11/6/01
  Converted to PIP input and to work on unlimited file sizes, 12/24/03