subimage(1) General Commands Manual 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.
-text (-t) OR -DifferenceTextFile File name
Output file for a copy of the difference statistics, which will
still be printed to standard out. The file will include the
header line and "all" line.
-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.
-frac (-f) OR -FractionalValues
Output an additional line expressing the summary statistics for
all sections as fractions of the data range of the two input
files.
-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.
IMOD 4.11.0 subimage(1)