assemblevol(1) General Commands Manual assemblevol(1)
NAME
assemblevol - assemble an image file from an array of subvolumes
SYNOPSIS
assemblevol
DESCRIPTION
Assemblevol will assemble a single MRC file from separate files that
form an array of subvolumes in X, Y, and Z. In effect, it can take
montaged images and compose them into single images, just as Reduce-
mont(1) can, but its advantage is that it can take the images from mul-
tiple files. Its primary use is for reassembling a tomogram after it
has been chopped into pieces, using the coordinates output by Tomo-
pieces(1). A second use to concatenate reprojections computed in par-
allel by Tilt.
If there is no overlap between the subvolumes to be assembled, then the
simplest way to run the program is with the -nxfiles, -nyfiles, and
-nzfiles options to indicate how many subvolumes there are in the three
dimensions. Otherwise, it is necessary to enter the starting and end-
ing coordinates to extract from the subvolumes at each position in X,
Y, and Z.
OPTIONS
Assemblevol 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.
-input (-i) OR -InputFile File name
Input file. Files must be entered in the order of left to right
in X, then bottom to top in Y, then lower to upper in Z. For
example, if there are files only in X and Y, enter all of the
files in the first row in Y in order by increasing X, then the
files in the second row, etc. Non-option arguments will also be
taken as input files after the ones specified by this option.
(Successive entries accumulate)
-output (-o) OR -OutputFile File name
Output file for assembled volume. If this entry is omitted, the
last non-option argument will be used for the output filename.
-xextract (-x) OR -StartEndToExtractInX Two integers
Starting and ending coordinates to extract at one file position
in X, numbered from 0, or 0,0 to use all pixels in X, or -1,-1
to use just the first pixel in X. If there is more than one
file position in X, this option must be entered for each posi-
tion in X, unless the number of files in X is entered with the
-nxfiles option and all pixels are to be taken from each file.
If neither this option nor -nxfiles is entered, the default is
to assume one position in X with all pixels used. Note that the
use of 0,0 to specify using all pixels requires the different
special entry of -1,-1 to use just the first pixel when the size
in X is greater than 1. (Successive entries accumulate)
-yextract (-y) OR -StartEndToExtractInY Two integers
Starting and ending coordinates to extract at one file position
in Y, numbered from 0, or 0,0 to use all pixels in Y. The same
rules apply to this option as to -xextract. (Successive entries
accumulate)
-zextract (-z) OR -StartEndToExtractInZ Two integers
Starting and ending coordinates to extract at one file position
in Z, numbered from 0, or 0,0 to use all pixels in Z. The same
rules apply to this option as to -xextract. (Successive entries
accumulate)
-nxfiles (-nx) OR -NumberOfFilesInX Integer
Number of input files in the X direction. This option can be
used if all pixels are to be used in X from all files; it cannot
be entered along with -xextract.
-nyfiles (-ny) OR -NumberOfFilesInY Integer
Number of input files in the Y direction. This option can be
used if all pixels are to be used in Y from all files; it cannot
be entered along with -yextract.
-nzfiles (-nz) OR -NumberOfFilesInZ Integer
Number of input files in the Z direction. This option can be
used if all pixels are to be used in Z from all files; it cannot
be entered along with -zextract.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries from file
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVE INPUT
If there are no command-line arguments, Assemblevol takes sequential
input the old way, with the following entries:
Name of output file for the assembled volume
Number of input files in the X, Y and Z dimensions
For each position in X, enter a line with the starting and ending X
index coordinates (numbered from 0) to be extracted from the files at
that position. These coordinates should be chosen to eliminate any
overlap between the files at successive positions. For example, if
there are two files in X, each 1000 pixels wide, and they overlap by 20
pixels, you would enter 0,989 and 10,999. If all the pixels are to be
taken from the files at a position, you can enter 0,0 for that posi-
tion. If the size in X is greater than 1, it is necessary to enter
-1,-1 to take just the first pixel.
Similarly, for each position in Y, enter a line with starting and end-
ing Y index coordinates to be extracted from files at that position, or
0,0 to use all pixels, or -1,-1 to use just the first pixel.
For each position in Z, enter a line with starting and ending Z index
coordinates to be extracted from files at that position, or 0,0 to use
all pixels, or -1,-1 to use just the first pixel.
The input file names, one per line, in order by increasing X, then
increasing Y, then increasing Z. For example, if there are files only
in X and Z, enter all of the files in the first row in Z in order by
increasing X, then the files in the second row, etc.
HISTORY
Written by David Mastronarde 3/1/01
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 assemblevol(1)