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. -xstats 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. Coordinates are numbered from 0; the default is the full area in X. -ystats 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. Coordinates 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 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 OR -ErrorSDLimit Floating point Exit with error if the overall standard deviation over the region where statistics were computed exceeds the given 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