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 mini-
       mum, maximum, mean, and standard deviation of each difference image.

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


       -afile (-af) 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 (-bf) 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 file-
              name with ~ appended).

       -output (-o) 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 (-mo) 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 (-as) OR -ASectionList   List of integer ranges
              List of sections in file A (numbered from 0, default is all sec-
              tions)

       -bsections (-bs) 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 (-z) OR -ZeroMeanOutput
              Make the mean of the output be zero for each section by sub-
              tracting the mean difference between sections from the differ-
              ence.

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

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

       -xstats (-x) OR -StatisticsXminAndMax    Two integers
              Minimum and maximum X for computing the minimum, maximum, mean
              and SD of the difference that are reported in the output. Coor-
              dinates are numbered from 0; the default is the full area in X.

       -ystats (-y) OR -StatisticsYminAndMax    Two integers
              Minimum and maximum Y for computing the minimum, maximum, mean
              and SD of the difference that are reported in the output.  Coor-
              dinates are numbered from 0; the default is the full area in Y.
              This entry and the next one do not affect the size of the output
              images; use Clip to obtain a difference volume from a subarea
              in one step.

       -minmax (-mi) OR -ErrorMinMaxLimit       Floating point
              Exit with error if the absolute value of the minimum or maximum
              exceeds the given value, over the region where statistics were
              computed.

       -sdlimit (-s) OR -ErrorSDLimit      Floating point
              Exit with error if the overall standard deviation over the
              region where statistics were computed exceeds the given value.

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

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

       -StandardInput
              Read parameter entries from standard input.


INTERACTIVE 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

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                         subimage(1)