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 signed integers, 2 for 32-bit float-
ing point, or 12 for 16-bit floating point). Bytes (mode 0) are
rarely suitable for a difference image since they are unsigned,
as is mode 6. The default is the mode of the input file,
although the default mode of floating point output for MRC files
is governed by the value of environment variable
IMOD_WRITE_FLOATS_16BIT. Mode 12 is allowed only if the output
format is MRC.
-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 5.2.0 subimage(1)