taperoutvol(1) General Commands Manual taperoutvol(1)
NAME
taperoutvol - to excise a subset of a volume, taper and pad outside
SYNOPSIS
taperoutvol [options] input_file output_file
DESCRIPTION
Taperoutvol will cut a subset out of an image volume, pad it into a
larger volume, and taper the intensity down to the mean value of the
volume over the extent of the padding region, i.e., from the edge of
the actual excised pixels to the edge of the new volume. None of the
original excised pixels are attenuated by this method. The resulting
volume will have dimensions suitable for taking the FFT unless the
-nofft option is entered. Its origin will be set so that a model built
on this subvolume in 3dmod should load correctly on the full volume.
OPTIONS
Taperoutvol uses the PIP package for input (see the manual page for
pip) and can still take sequential input interactively, to maintain
compatibility with old command files. 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 -). Options can be
abbreviated to unique letters; the currently valid abbreviations for
short names are shown in parentheses.
-input (-i) OR -InputFile File name
Input image file
-output (-o) OR -OutputFile File name
Output image file
-xminmax (-x) OR -XMinAndMax Two integers
Starting and ending X index coordinates to extract, numbered
from 0. The default is the whole width in X.
-yminmax (-y) OR -YMinAndMax Two integers
Starting and ending Y index coordinates to extract, numbered
from 0. The default is the whole height in Y.
-zminmax (-z) OR -ZMinAndMax Two integers
Starting and ending Z index coordinates to extract, numbered
from 0. The default is the whole depth in Z.
-taper (-t) OR -TaperPadsInXYZ Three integers
Number of pixels over which to taper and pad the patches in X, Y
and Z. The default is 0. Unless the -nofft option is entered,
the amount of tapering in any dimension may be increased to make
that dimension suitable for taking an FFT.
-nofft (-nof) OR -NoFFTSizes
Do not adjust the padding to give sizes suitable for an FFT.
This option is particularly important if you want no tapering
and padding.
-noise (-noi) OR -NoisePadding
Use tapered noise based on nearby pixels along the edge of an
image to pad the images. The default is to pad with a simple
taper that makes streaks outside the edge of the image.
-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, Taperoutvol takes sequential
input the old way, with the following entries:
Inputs to the program:
Name of input file
Name of output file
The starting and ending X index coordinates (number from 0), the start-
ing and ending Y index coordinates, and the starting and ending Z index
coordinates to extract. The default is the whole volume.
The width of the borders, in X, Y, and Z, with which to pad the image
block. Borders will be made larger as necessary to make the output
image size suitable for taking a 3D FFT, with the exception that if a
single Z slice is requested with no padding, only a single slice is
produced without padding.
The program will stop with an error message if memory cannot be allo-
cated for the output image, or if the subset is not entirely within the
input volume.
HISTORY
Written by David Mastronarde 3/1/01
Converted to PIP, 1/8/10
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 taperoutvol(1)